Nothing
## Julia Bischof
## 15-10-2015
clones.filterSize<-function(clones.tab=NULL, column=NULL, number=NULL, propOfClones=NULL, propOfSequences=NULL,
method=c("two.tailed","upper.tail","lower.tail")){
if(length(clones.tab)==0){
stop("--> Clones.tab is missing")
}
if(sum(c(length(number),length(propOfClones),length(propOfSequences)))>1 || sum(c(length(number),length(propOfClones),length(propOfSequences)))==0){
stop("--> Please input one (!) filter criteria")
}
if(length(column)!=1){
stop("--> Please insert column number of colname of column, which includes clone sizes (f.e. total_number_of_sequences)")
}
if(length(method)!=1 || !(method %in% c("two.tailed","upper.tail","lower.tail"))){
stop("--> Method (two.tailed,upper.tail,lower.tail) is missing")
}
clones.tab<-clones.tab[order(as.numeric(clones.tab[,column]),decreasing = T),]
if(length(number)>0){
if(method=="two.tailed"){
clones.up<-clones.tab[1:number,]
clones.low<-clones.tab[(nrow(clones.tab)-number+1):nrow(clones.tab),]
}else if(method=="upper.tail"){
clones.up<-clones.tab[1:number,]
}else if(method=="lower.tail"){
clones.low<-clones.tab[(nrow(clones.tab)-number+1):nrow(clones.tab),]
}
}
if(length(propOfClones)>0){
tr<-round(propOfClones*nrow(clones.tab))
if(method=="two.tailed"){
clones.up<-clones.tab[1:tr,]
clones.low<-clones.tab[(nrow(clones.tab)-tr+1):nrow(clones.tab),]
}else if(method=="upper.tail"){
clones.up<-clones.tab[1:tr,]
}else if(method=="lower.tail"){
clones.low<-clones.tab[(nrow(clones.tab)-tr+1):nrow(clones.tab),]
}
}
if(length(propOfSequences)>0){
tr<-as.numeric(sum(as.numeric(clones.tab[,column]),na.rm=T)*propOfSequences)
if(method=="two.tailed"){
clones.up<-clones.tab[which(clones.tab[,column]>tr),]
clones.low<-clones.tab[which(clones.tab[,column]<=tr),]
}else if(method=="upper.tail"){
clones.up<-clones.tab[which(clones.tab[,column]>tr),]
}else if(method=="lower.tail"){
clones.low<-clones.tab[which(clones.tab[,column]<=tr),]
}
}
if(method=="two.tailed"){
outlist<-list(clones.up, clones.low)
names(outlist)<-c("upper.tail","lower.tail")
return(outlist)
}else if(method=="upper.tail"){
return(clones.up)
}else if(method=="lower.tail"){
return(clones.low)
}
}
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