R/p53sf.R
In tomateba/p53retriever: detection and display of p53 putative response elements (REs) on DNA sequences
#' Locate candidate p53 responsive elements (full and half) on a DNA sequence
#'
#' @param seq.ini A character string containing the sequence. The sequence must be composed exclusively of DNA bases (a,c,t,g)
#' @return A dataframe containing the responsive elements located on the input sequence.
#' @export
# Halves and full matrix
#--------------------------------
p53sf<-function(seq.ini){
data(bkg.models)
subject<-DNAString(seq.ini)
couples.matrix<-NULL
occurrences.matrix<-NULL
couples.flag<-0
plus.matches <- matchPWM(pwm.1, subject, min.score="80%")
if(length(plus.matches)>0){
sequence<-as.character(plus.matches)
start.seq<-start(plus.matches)
stop.seq<-end(plus.matches)
n.mut<-unlist(lapply(sequence, function(x) ((1000-PWMscoreStartingAt(pwm.1, x, starting.at=1))/100)))
#ww<-unlist(lapply(sequence, function(x) substr(x,5,6)))
occurrences.matrix<-cbind(sequence,start.seq,stop.seq,n.mut)
colnames(occurrences.matrix)<-c("seq","start","stop","n.mut")
for(n in 1:nrow(occurrences.matrix)){
n.couples.run<-which(
(is.between(as.numeric(occurrences.matrix[,"start"])-as.numeric(occurrences.matrix[n,"start"]),9,24))&
(as.numeric(occurrences.matrix[,"n.mut"])+as.numeric(occurrences.matrix[n,"n.mut"])<(3)))
if(length(n.couples.run)>0){
couples.flag<-1
first<-t(matrix(rep(occurrences.matrix[n,],length(n.couples.run)),ncol=length(n.couples.run)))
second<-matrix(occurrences.matrix[n.couples.run,],nrow=length(n.couples.run))
couples.matrix.run<-cbind(first, second, as.numeric(second[,2])-(as.numeric(first[,3])+1),
as.numeric(second[,4])+as.numeric(first[,4]))
couples.matrix<-rbind(couples.matrix,couples.matrix.run)
}
}
}
#------------------------------------------------------
### half sites
#------------------------------------------------------
halves.matrix<-NULL
resume.matrix.halves<-NULL
if(length(which(occurrences.matrix[,"n.mut"]=="0"))>0) {
halves.matrix<-matrix(occurrences.matrix[occurrences.matrix[,"n.mut"]=="0",],nrow=length(which(occurrences.matrix[,"n.mut"]=="0")))
ww.half<-apply(halves.matrix,1,function(x) substr(x[1],5,6))
halves.matrix[,ncol(halves.matrix)]<-ww.half
colnames(halves.matrix)<-c("sequence","start","stop","WW1")
n.mut.tot<-apply(halves.matrix,1,function(x) ((1000-PWMscoreStartingAt(pwm.6, DNAString(x["sequence"]), starting.at=1))/100))
if(length(which(n.mut.tot<1))>0){
halves.matrix<-matrix(halves.matrix[which(n.mut.tot==0),],nrow=length(which(n.mut.tot==0)))
colnames(halves.matrix)<-c("sequence","start","stop","WW1")
WW2<-rep("",nrow(halves.matrix))
spacer<-rep(0,nrow(halves.matrix))
n.mut.tot<-rep(0,nrow(halves.matrix))
mutations<-rep("0000000000",nrow(halves.matrix))
halves.matrix.2<-cbind(as.data.frame(halves.matrix),WW2,spacer,mutations,n.mut.tot)
halves.matrix.2[,"start"]<-as.numeric(halves.matrix[,"start"])
halves.matrix.2[,"stop"]<-as.numeric(halves.matrix[,"stop"])
halves.matrix.2[,"spacer"]<-as.numeric(spacer)
halves.matrix.2[,"n.mut.tot"]<-as.numeric(n.mut.tot)
halves.matrix.2<-transform(halves.matrix.2,
sequence=as.character(sequence),
mutations=as.character(mutations),
WW2=as.character(WW2),
WW1=as.character(WW1))
halves.matrix.2<-halves.matrix.2[,c("start","stop","spacer","n.mut.tot","sequence","mutations","WW1","WW2")]
grades<-rep(1,length=nrow(halves.matrix.2))
grades[halves.matrix.2[,"WW1"]=="AT"]<-2
labels<-rep("half",length=nrow(halves.matrix.2))
resume.matrix.halves<-cbind(halves.matrix.2,labels,grades)
}
}
#---------------------------------------------------------------------
# Analysis of full sites
#---------------------------------------------------------------------
resume.matrix.full<-NULL
if(couples.flag==1){
colnames(couples.matrix)<-c("seq.1","start.1","stop.1","n.mut.1","seq.2","start.2","stop.2","n.mut.2","spacer","n.mut.tot")
work.matrix<-couples.matrix
pattern.matrix<-matrix(0,nrow=nrow(work.matrix),ncol=20)
ww.matrix<-matrix("",nrow=nrow(work.matrix),ncol=2)
colnames(pattern.matrix)<-c("R1","R2","R3","C1","W1","W2","G1","Y1","Y2","Y3",
"R4","R5","R6","C2","W3","W4","G2","Y4","Y5","Y6")
colnames(ww.matrix)<-c("WW1","WW2")
double.pwm<-cbind(pwm.6,pwm.6)
for(p in (1:nrow(work.matrix))){
pair.seq<-paste(couples.matrix[p,"seq.1"],couples.matrix[p,"seq.2"],sep="")
line<-vector(mode="numeric",length=20)
for (l in (1:20)){
letter<-substr(pair.seq,l,l)
line[l]<-as.numeric(double.pwm[as.character(letter),l]=="0")
}
pattern.matrix[p,]<-line
ww.matrix[p,1]<-as.character(substr(pair.seq,5,6))
ww.matrix[p,2]<-as.character(substr(pair.seq,15,16))
}
pattern<-as.data.frame(pattern.matrix)
ww<-as.data.frame(ww.matrix)
couple.matrix<-cbind(work.matrix,pattern,ww)
sequence<-apply(couple.matrix,1,function(x) toupper(substr(seq.ini,x["start.1"],x["stop.2"])))
mutations<-apply(couple.matrix,1,function(x) paste(paste(x[11:20],collapse=""),paste(rep("n",length=x["spacer"]),collapse=""),paste(x[21:30],collapse=""),sep=""))
smart.matrix<-cbind(matrix(work.matrix[,c("start.1","stop.2","spacer","n.mut.tot")],nrow=nrow(couple.matrix)),sequence,mutations,ww,pattern)
colnames(smart.matrix)[1:2]<-c("start","stop")
smart.matrix[,"n.mut.tot"]<-rowSums(pattern)
smart.matrix[,"spacer"]<-as.numeric(couples.matrix[,"spacer"])
smart.matrix[,"start"]<-as.numeric(couples.matrix[,"start.1"])
smart.matrix[,"stop"]<-as.numeric(couples.matrix[,"stop.2"])
class.matrix<-transform(smart.matrix,
sequence=as.character(sequence),
mutations=as.character(mutations),
WW1=as.character(WW1),
WW2=as.character(WW2))
grades<-vector(mode="integer",length=nrow(class.matrix))
labels<-vector(mode="character",length=nrow(class.matrix))
#-----------------------
# Rules for full sites
#-----------------------
#1) O
#----------------------------------------------------
labels[which(class.matrix[,"n.mut.tot"]==0)]<-"O"
#-----------------------------------------------------
grades[which(class.matrix[,"n.mut.tot"]==0)]<-2
grades[which((class.matrix[,"n.mut.tot"]==0)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==0)
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==0)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-5
#2) A
#----------------------------------------------------
mut.cols<-c("C1","G2","C2","G1")
labels[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-"A"
#----------------------------------------------------
mut.cols<-c("C1","G2")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]!=0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
mut.cols<-c("C2","G1")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#3) B
#----------------------------------------------------
mut.cols<-c("W1","W2","W3","W4")
labels[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-"B"
#----------------------------------------------------
mut.cols<-c("W1","W4")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
mut.cols<-c("W2","W3")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#4) C
#----------------------------------------------------
mut.cols<-c("R1","R4","Y3","Y6")
labels[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-"C"
#----------------------------------------------------
mut.cols<-c("R1","Y6")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-5
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
mut.cols<-c("R4","Y3")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-5
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
#5) D
#----------------------------------------------------
mut.cols<-c("R2","R3","R5","R6","Y1","Y2","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-"D"
#----------------------------------------------------
mut.cols<-c("R2","R3","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
mut.cols<-c("R5","R6","Y1","Y2")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
#------------------------------------
#6) AA
#----------------------------------------------------
mut.cols<-c("C1","G1","C2","G2")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-"AA"
#----------------------------------------------------
# same half-site
mut.cols<-c("C1","G1","C2","G2")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
# different half-site
#----------------------------------------------------
mut.cols<-c("C1","G1","C2","G2")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])==1))]<-1
#----------------------------------------------------
# 7) BB
#----------------------------------------------------
mut.cols<-c("W1","W2","W3","W4")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-"BB"
#----------------------------------------------------
# same half site
mut.cols<-c("W1","W2","W3","W4")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#----------------------------------------------------
#different half site
mut.cols<-c("W1","W2","W3","W4")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])==1)
&(class.matrix[,"spacer"]==0))]<-2
#----------------------------------------------------
# 8) AB
#----------------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("W1","W2","W3","W4")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"AB"
#-----------------------------------------------------------
# same half site
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("W1","W2","W3","W4")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-2
#----------------------------------------------------
# 1st or 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,4)])])==2)))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,4)])])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]>0))]<-2
#----------------------------------------------------
# all 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-3
#------------------------------------------------------
# 9) BD
#----------------------------------------------------
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"BD"
#----------------------------------------------------
# same half site
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]>0))]<-2
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-2
#----------------------------------------------------
# 1st or 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2)))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]>0))]<-2
#----------------------------------------------------
# All 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0)
)]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]>0)
)]<-2
#--------------------------------------------------
# 10) AD
#----------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"AD"
#----------------------------------------------------
# same half site
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
#----------------------------------------------------
# 1st or 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2)))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
#--------------------------------------------------
# All 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0)
)]<-4
#-------------------------------------------------------------------------------------
# 11) DD
#----------------------------------------------------
mut.cols<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-"DD"
#----------------------------------------------------
# same half site
mut.cols<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#----------------------------------------------------
# 1st or 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[c(1,2,7,8)]])==2))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[c(1,2,7,8)]])==2)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[c(1,2,7,8)]])==2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[c(1,2,7,8)]])==2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#--------------------------------------------------
# All 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((rowSums(class.matrix[,mut.cols[c(1,2)]])==2)|(rowSums(class.matrix[,mut.cols[c(7,8)]])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((rowSums(class.matrix[,mut.cols[c(1,2)]])==2)|(rowSums(class.matrix[,mut.cols[c(7,8)]])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((rowSums(class.matrix[,mut.cols[c(1,2)]])==2)|(rowSums(class.matrix[,mut.cols[c(7,8)]])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
#--------------------------------------------------
# 12) CC
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-"CC"
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-5
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-3
#--------------------------------------------------
# 13) BC
#----------------------------------------------------
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"BC"
#----------------------------------------------------
# same half site
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#----------------------------------------------------
# all 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#--------------------------------------------------
# 14) CD
#----------------------------------------------------
mut.cols.1<-c("R1","Y3","R4","Y6")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"CD"
#----------------------------------------------------
mut.cols.1<-c("R1","Y3","R4","Y6")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#----------------------------------------------------
# 15) AC
#----------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"AC"
#----------------------------------------------------
# same half site
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#----------------------------------------------------
# all 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
#--------------------------------------------------
### 16) A+C+C
#----------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2))]<-"ACC"
#----------------------------------------------------
# A in C1 or G2
#----------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-4
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-2
#----------------------------------------------------
# A in G1 or C2
#----------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
&(class.matrix[,"spacer"]==0)
)]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-3
#------------------------------------------------------
# 17) BCC
#----------------------------------------------------
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2))]<-"BCC"
#----------------------------------------------------
# B in W1 or W4
#----------------------------------------------------
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-4
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-2
#----------------------------------------------------
# B in W2 or W3
#----------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
&(class.matrix[,"spacer"]==0)
)]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-3
#--------------------------------------------------
### 18) CCC
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3))]<-"CCC"
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#--------------------------------------------------
#------------------------------------------------------
# 19) CCD
#----------------------------------------------------
mut.cols.1<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2))]<-"CCD"
#----------------------------------------------------
# D in first or last quarter
#----------------------------------------------------
mut.cols.1<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==1)
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-4
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-2
#----------------------------------------------------
# D in W2 or W3
#----------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==0)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==0)
&(class.matrix[,"spacer"]==0)
)]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==0)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-3
#--------------------------------------------------
### 20) CCCC
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4))]<-"CCCC"
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4))]<-1
grades[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#-------------------------------------------------
#------------------------------------------------
### 21) ABC
#First quarter
#---------------------------------------------------------
mut.cols.1<-c("C1","W1")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"ABC"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#-----------------------------------------------------
#Fourth quarter
#---------------------------------------------------------
mut.cols.1<-c("G2","W4")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"ABC"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#-----------------------------------------------------
#------------------------------------------------
### 22) BCD
#First quarter
#---------------------------------------------------------
mut.cols.1<-c("W1","W1")
mut.cols.2<-c("R2","R3")
mut.cols.3<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-"BCD"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#--------------------------------------------------------
#Fourth quarter
#---------------------------------------------------------
mut.cols.1<-c("W4","W4")
mut.cols.2<-c("Y4","Y5")
mut.cols.3<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-"BCD"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------------------
#------------------------------------------------
### 23) ACD
#First quarter
#--------------------------------------------------------------
mut.cols.1<-c("C1","C1")
mut.cols.2<-c("R2","R3")
mut.cols.3<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-"ACD"
#--------------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#--------------------------------------------------------
#Fourth quarter
#--------------------------------------------------------------
mut.cols.1<-c("G2","G2")
mut.cols.2<-c("Y4","Y5")
mut.cols.3<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-"ACD"
#--------------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#--------------------------------------------------------
#-------------------
### 24) CDD
#-------------------
# all D and C in the 1st or 4th quarter
mut.cols.1<-c("R2","R3","Y4","Y5")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"CDD"
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#First quarter
#---------------------------------------------------------
mut.cols.1<-c("R2","R3")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"CDD"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#-----------------------------------------------------
#Fourth quarter
#---------------------------------------------------------
mut.cols.1<-c("Y4","Y5")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"CDD"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#-----------------------------------------------------
resume.matrix<-cbind(class.matrix,labels,grades)
if(length(which(resume.matrix[,"grades"]>0))>0){
resume.matrix.full<-resume.matrix[which(resume.matrix[,"grades"]>0),c("start","stop","spacer","n.mut.tot","sequence","mutations","WW1","WW2","labels","grades")]
}
}
pre.complete<-rbind(resume.matrix.full,resume.matrix.halves)
return(pre.complete)
}
tomateba/p53retriever documentation built on May 31, 2019, 6:10 p.m.
R Package Documentation
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#' Locate candidate p53 responsive elements (full and half) on a DNA sequence
#'
#' @param seq.ini A character string containing the sequence. The sequence must be composed exclusively of DNA bases (a,c,t,g)
#' @return A dataframe containing the responsive elements located on the input sequence.
#' @export
# Halves and full matrix
#--------------------------------
p53sf<-function(seq.ini){
data(bkg.models)
subject<-DNAString(seq.ini)
couples.matrix<-NULL
occurrences.matrix<-NULL
couples.flag<-0
plus.matches <- matchPWM(pwm.1, subject, min.score="80%")
if(length(plus.matches)>0){
sequence<-as.character(plus.matches)
start.seq<-start(plus.matches)
stop.seq<-end(plus.matches)
n.mut<-unlist(lapply(sequence, function(x) ((1000-PWMscoreStartingAt(pwm.1, x, starting.at=1))/100)))
#ww<-unlist(lapply(sequence, function(x) substr(x,5,6)))
occurrences.matrix<-cbind(sequence,start.seq,stop.seq,n.mut)
colnames(occurrences.matrix)<-c("seq","start","stop","n.mut")
for(n in 1:nrow(occurrences.matrix)){
n.couples.run<-which(
(is.between(as.numeric(occurrences.matrix[,"start"])-as.numeric(occurrences.matrix[n,"start"]),9,24))&
(as.numeric(occurrences.matrix[,"n.mut"])+as.numeric(occurrences.matrix[n,"n.mut"])<(3)))
if(length(n.couples.run)>0){
couples.flag<-1
first<-t(matrix(rep(occurrences.matrix[n,],length(n.couples.run)),ncol=length(n.couples.run)))
second<-matrix(occurrences.matrix[n.couples.run,],nrow=length(n.couples.run))
couples.matrix.run<-cbind(first, second, as.numeric(second[,2])-(as.numeric(first[,3])+1),
as.numeric(second[,4])+as.numeric(first[,4]))
couples.matrix<-rbind(couples.matrix,couples.matrix.run)
}
}
}
#------------------------------------------------------
### half sites
#------------------------------------------------------
halves.matrix<-NULL
resume.matrix.halves<-NULL
if(length(which(occurrences.matrix[,"n.mut"]=="0"))>0) {
halves.matrix<-matrix(occurrences.matrix[occurrences.matrix[,"n.mut"]=="0",],nrow=length(which(occurrences.matrix[,"n.mut"]=="0")))
ww.half<-apply(halves.matrix,1,function(x) substr(x[1],5,6))
halves.matrix[,ncol(halves.matrix)]<-ww.half
colnames(halves.matrix)<-c("sequence","start","stop","WW1")
n.mut.tot<-apply(halves.matrix,1,function(x) ((1000-PWMscoreStartingAt(pwm.6, DNAString(x["sequence"]), starting.at=1))/100))
if(length(which(n.mut.tot<1))>0){
halves.matrix<-matrix(halves.matrix[which(n.mut.tot==0),],nrow=length(which(n.mut.tot==0)))
colnames(halves.matrix)<-c("sequence","start","stop","WW1")
WW2<-rep("",nrow(halves.matrix))
spacer<-rep(0,nrow(halves.matrix))
n.mut.tot<-rep(0,nrow(halves.matrix))
mutations<-rep("0000000000",nrow(halves.matrix))
halves.matrix.2<-cbind(as.data.frame(halves.matrix),WW2,spacer,mutations,n.mut.tot)
halves.matrix.2[,"start"]<-as.numeric(halves.matrix[,"start"])
halves.matrix.2[,"stop"]<-as.numeric(halves.matrix[,"stop"])
halves.matrix.2[,"spacer"]<-as.numeric(spacer)
halves.matrix.2[,"n.mut.tot"]<-as.numeric(n.mut.tot)
halves.matrix.2<-transform(halves.matrix.2,
sequence=as.character(sequence),
mutations=as.character(mutations),
WW2=as.character(WW2),
WW1=as.character(WW1))
halves.matrix.2<-halves.matrix.2[,c("start","stop","spacer","n.mut.tot","sequence","mutations","WW1","WW2")]
grades<-rep(1,length=nrow(halves.matrix.2))
grades[halves.matrix.2[,"WW1"]=="AT"]<-2
labels<-rep("half",length=nrow(halves.matrix.2))
resume.matrix.halves<-cbind(halves.matrix.2,labels,grades)
}
}
#---------------------------------------------------------------------
# Analysis of full sites
#---------------------------------------------------------------------
resume.matrix.full<-NULL
if(couples.flag==1){
colnames(couples.matrix)<-c("seq.1","start.1","stop.1","n.mut.1","seq.2","start.2","stop.2","n.mut.2","spacer","n.mut.tot")
work.matrix<-couples.matrix
pattern.matrix<-matrix(0,nrow=nrow(work.matrix),ncol=20)
ww.matrix<-matrix("",nrow=nrow(work.matrix),ncol=2)
colnames(pattern.matrix)<-c("R1","R2","R3","C1","W1","W2","G1","Y1","Y2","Y3",
"R4","R5","R6","C2","W3","W4","G2","Y4","Y5","Y6")
colnames(ww.matrix)<-c("WW1","WW2")
double.pwm<-cbind(pwm.6,pwm.6)
for(p in (1:nrow(work.matrix))){
pair.seq<-paste(couples.matrix[p,"seq.1"],couples.matrix[p,"seq.2"],sep="")
line<-vector(mode="numeric",length=20)
for (l in (1:20)){
letter<-substr(pair.seq,l,l)
line[l]<-as.numeric(double.pwm[as.character(letter),l]=="0")
}
pattern.matrix[p,]<-line
ww.matrix[p,1]<-as.character(substr(pair.seq,5,6))
ww.matrix[p,2]<-as.character(substr(pair.seq,15,16))
}
pattern<-as.data.frame(pattern.matrix)
ww<-as.data.frame(ww.matrix)
couple.matrix<-cbind(work.matrix,pattern,ww)
sequence<-apply(couple.matrix,1,function(x) toupper(substr(seq.ini,x["start.1"],x["stop.2"])))
mutations<-apply(couple.matrix,1,function(x) paste(paste(x[11:20],collapse=""),paste(rep("n",length=x["spacer"]),collapse=""),paste(x[21:30],collapse=""),sep=""))
smart.matrix<-cbind(matrix(work.matrix[,c("start.1","stop.2","spacer","n.mut.tot")],nrow=nrow(couple.matrix)),sequence,mutations,ww,pattern)
colnames(smart.matrix)[1:2]<-c("start","stop")
smart.matrix[,"n.mut.tot"]<-rowSums(pattern)
smart.matrix[,"spacer"]<-as.numeric(couples.matrix[,"spacer"])
smart.matrix[,"start"]<-as.numeric(couples.matrix[,"start.1"])
smart.matrix[,"stop"]<-as.numeric(couples.matrix[,"stop.2"])
class.matrix<-transform(smart.matrix,
sequence=as.character(sequence),
mutations=as.character(mutations),
WW1=as.character(WW1),
WW2=as.character(WW2))
grades<-vector(mode="integer",length=nrow(class.matrix))
labels<-vector(mode="character",length=nrow(class.matrix))
#-----------------------
# Rules for full sites
#-----------------------
#1) O
#----------------------------------------------------
labels[which(class.matrix[,"n.mut.tot"]==0)]<-"O"
#-----------------------------------------------------
grades[which(class.matrix[,"n.mut.tot"]==0)]<-2
grades[which((class.matrix[,"n.mut.tot"]==0)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==0)
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==0)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-5
#2) A
#----------------------------------------------------
mut.cols<-c("C1","G2","C2","G1")
labels[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-"A"
#----------------------------------------------------
mut.cols<-c("C1","G2")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]!=0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
mut.cols<-c("C2","G1")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#3) B
#----------------------------------------------------
mut.cols<-c("W1","W2","W3","W4")
labels[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-"B"
#----------------------------------------------------
mut.cols<-c("W1","W4")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
mut.cols<-c("W2","W3")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#4) C
#----------------------------------------------------
mut.cols<-c("R1","R4","Y3","Y6")
labels[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-"C"
#----------------------------------------------------
mut.cols<-c("R1","Y6")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-5
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
mut.cols<-c("R4","Y3")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-5
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
#5) D
#----------------------------------------------------
mut.cols<-c("R2","R3","R5","R6","Y1","Y2","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-"D"
#----------------------------------------------------
mut.cols<-c("R2","R3","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------
mut.cols<-c("R5","R6","Y1","Y2")
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==1)
&(rowSums(class.matrix[,mut.cols])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
#------------------------------------
#6) AA
#----------------------------------------------------
mut.cols<-c("C1","G1","C2","G2")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-"AA"
#----------------------------------------------------
# same half-site
mut.cols<-c("C1","G1","C2","G2")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
# different half-site
#----------------------------------------------------
mut.cols<-c("C1","G1","C2","G2")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])==1))]<-1
#----------------------------------------------------
# 7) BB
#----------------------------------------------------
mut.cols<-c("W1","W2","W3","W4")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-"BB"
#----------------------------------------------------
# same half site
mut.cols<-c("W1","W2","W3","W4")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])!=1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#----------------------------------------------------
#different half site
mut.cols<-c("W1","W2","W3","W4")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:2]])==1)
&(class.matrix[,"spacer"]==0))]<-2
#----------------------------------------------------
# 8) AB
#----------------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("W1","W2","W3","W4")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"AB"
#-----------------------------------------------------------
# same half site
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("W1","W2","W3","W4")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-2
#----------------------------------------------------
# 1st or 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,4)])])==2)))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,4)])])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]>0))]<-2
#----------------------------------------------------
# all 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-3
#------------------------------------------------------
# 9) BD
#----------------------------------------------------
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"BD"
#----------------------------------------------------
# same half site
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]>0))]<-2
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-2
#----------------------------------------------------
# 1st or 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2)))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]>0))]<-2
#----------------------------------------------------
# All 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0)
)]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]>0)
)]<-2
#--------------------------------------------------
# 10) AD
#----------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"AD"
#----------------------------------------------------
# same half site
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])!=1)
&(class.matrix[,"spacer"]>0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:4])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
#----------------------------------------------------
# 1st or 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2)))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1,4)],mut.cols.2[c(1,2,7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
#--------------------------------------------------
# All 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1,2)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(7,8)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0)
)]<-4
#-------------------------------------------------------------------------------------
# 11) DD
#----------------------------------------------------
mut.cols<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-"DD"
#----------------------------------------------------
# same half site
mut.cols<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[1:4]])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#----------------------------------------------------
# 1st or 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[c(1,2,7,8)]])==2))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[c(1,2,7,8)]])==2)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[c(1,2,7,8)]])==2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(rowSums(class.matrix[,mut.cols[c(1,2,7,8)]])==2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#--------------------------------------------------
# All 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((rowSums(class.matrix[,mut.cols[c(1,2)]])==2)|(rowSums(class.matrix[,mut.cols[c(7,8)]])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((rowSums(class.matrix[,mut.cols[c(1,2)]])==2)|(rowSums(class.matrix[,mut.cols[c(7,8)]])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((rowSums(class.matrix[,mut.cols[c(1,2)]])==2)|(rowSums(class.matrix[,mut.cols[c(7,8)]])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
#--------------------------------------------------
# 12) CC
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-"CC"
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-5
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols])==2)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-3
#--------------------------------------------------
# 13) BC
#----------------------------------------------------
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"BC"
#----------------------------------------------------
# same half site
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#----------------------------------------------------
# all 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#--------------------------------------------------
# 14) CD
#----------------------------------------------------
mut.cols.1<-c("R1","Y3","R4","Y6")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"CD"
#----------------------------------------------------
mut.cols.1<-c("R1","Y3","R4","Y6")
mut.cols.2<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#----------------------------------------------------
# 15) AC
#----------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"AC"
#----------------------------------------------------
# same half site
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])!=1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#----------------------------------------------------
#different half site
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,c(mut.cols.1[1:2],mut.cols.2[1:2])])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#----------------------------------------------------
# all 1st or all 4th quarter
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==2)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==1)
&((rowSums(class.matrix[,c(mut.cols.1[c(1)],mut.cols.2[c(1)])])==2)|(rowSums(class.matrix[,c(mut.cols.1[c(4)],mut.cols.2[c(4)])])==2))
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-4
#--------------------------------------------------
### 16) A+C+C
#----------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2))]<-"ACC"
#----------------------------------------------------
# A in C1 or G2
#----------------------------------------------------
mut.cols.1<-c("C1","G1","C2","G2")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-4
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-2
#----------------------------------------------------
# A in G1 or C2
#----------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
&(class.matrix[,"spacer"]==0)
)]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-3
#------------------------------------------------------
# 17) BCC
#----------------------------------------------------
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2))]<-"BCC"
#----------------------------------------------------
# B in W1 or W4
#----------------------------------------------------
mut.cols.1<-c("W1","W2","W3","W4")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-4
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-2
#----------------------------------------------------
# B in W2 or W3
#----------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
&(class.matrix[,"spacer"]==0)
)]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,4)])])==0)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-3
#--------------------------------------------------
### 18) CCC
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3))]<-"CCC"
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3)
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-4
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols])==3)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#--------------------------------------------------
#------------------------------------------------------
# 19) CCD
#----------------------------------------------------
mut.cols.1<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
mut.cols.2<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2))]<-"CCD"
#----------------------------------------------------
# D in first or last quarter
#----------------------------------------------------
mut.cols.1<-c("R2","R3","Y1","Y2","R5","R6","Y4","Y5")
mut.cols.2<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==1)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==1)
&(class.matrix[,"spacer"]==0)
)]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-4
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-2
#----------------------------------------------------
# D in W2 or W3
#----------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==0)
)]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==0)
&(class.matrix[,"spacer"]==0)
)]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==1)
&(rowSums(class.matrix[,mut.cols.2])==2)
&(rowSums(class.matrix[,c(mut.cols.1[c(1,2,7,8)])])==0)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
)]<-3
#--------------------------------------------------
### 20) CCCC
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
labels[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4))]<-"CCCC"
#----------------------------------------------------
mut.cols<-c("R1","Y3","R4","Y6")
grades[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4))]<-1
grades[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]==0))]<-3
grades[which((class.matrix[,"n.mut.tot"]==4)
&(rowSums(class.matrix[,mut.cols])==4)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT"))
&(class.matrix[,"spacer"]%in%c(1,2)))]<-2
#-------------------------------------------------
#------------------------------------------------
### 21) ABC
#First quarter
#---------------------------------------------------------
mut.cols.1<-c("C1","W1")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"ABC"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#-----------------------------------------------------
#Fourth quarter
#---------------------------------------------------------
mut.cols.1<-c("G2","W4")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"ABC"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#-----------------------------------------------------
#------------------------------------------------
### 22) BCD
#First quarter
#---------------------------------------------------------
mut.cols.1<-c("W1","W1")
mut.cols.2<-c("R2","R3")
mut.cols.3<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-"BCD"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#--------------------------------------------------------
#Fourth quarter
#---------------------------------------------------------
mut.cols.1<-c("W4","W4")
mut.cols.2<-c("Y4","Y5")
mut.cols.3<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-"BCD"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#------------------------------------------------
#------------------------------------------------
### 23) ACD
#First quarter
#--------------------------------------------------------------
mut.cols.1<-c("C1","C1")
mut.cols.2<-c("R2","R3")
mut.cols.3<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-"ACD"
#--------------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#--------------------------------------------------------
#Fourth quarter
#--------------------------------------------------------------
mut.cols.1<-c("G2","G2")
mut.cols.2<-c("Y4","Y5")
mut.cols.3<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-"ACD"
#--------------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(rowSums(class.matrix[,mut.cols.3])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
#--------------------------------------------------------
#-------------------
### 24) CDD
#-------------------
# all D and C in the 1st or 4th quarter
mut.cols.1<-c("R2","R3","Y4","Y5")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"CDD"
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#First quarter
#---------------------------------------------------------
mut.cols.1<-c("R2","R3")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"CDD"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#-----------------------------------------------------
#Fourth quarter
#---------------------------------------------------------
mut.cols.1<-c("Y4","Y5")
mut.cols.2<-c("R1","Y6")
labels[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-"CDD"
#-----------------------------------------------------------
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1))]<-1
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0))]<-2
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]==0)
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-3
grades[which((class.matrix[,"n.mut.tot"]==3)
&(rowSums(class.matrix[,mut.cols.1])==2)
&(rowSums(class.matrix[,mut.cols.2])==1)
&(class.matrix[,"spacer"]%in%c(1,2))
&((class.matrix[,"WW1"]=="AT")|(class.matrix[,"WW2"]=="AT")))]<-2
#-----------------------------------------------------
resume.matrix<-cbind(class.matrix,labels,grades)
if(length(which(resume.matrix[,"grades"]>0))>0){
resume.matrix.full<-resume.matrix[which(resume.matrix[,"grades"]>0),c("start","stop","spacer","n.mut.tot","sequence","mutations","WW1","WW2","labels","grades")]
}
}
pre.complete<-rbind(resume.matrix.full,resume.matrix.halves)
return(pre.complete)
}
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