Nothing
getSegChr <- function(bb.chr=NULL,ll.chr=NULL,sam.col=5,control=TRUE, thr.hets=0.1, bin=1000,data.type='copy',controlOne=0){
chr<-bb.chr[1,2]
cat('processing ',chr,'\n')
#desired input for bb.chr and ll.chr:
##row_names, col1, col2, col3,... coln
## SNP id, chr, pos, sample1,... samplen
## if is.paired is TRUE, for TCGA samples only, i.e. when is.paired=T, is.tcga is T
## if is.uniform is TRUE, then all samples share same segments, and the first column of segment file will not be used
if(nrow(bb.chr)!=nrow(ll.chr))stop("Incompatible markers for BAF and LogR!")
nsam<-ncol(bb.chr)
bb.chr<-bb.chr[order(as.numeric(bb.chr[,3])),]
ll.chr<-ll.chr[order(as.numeric(ll.chr[,3])),]
#bb.chr=bb.chr[order(bb.chr[,2]),]
dat.chr<-c()
i<-sam.col
sampleID<-colnames(bb.chr)[i:nsam]
if(control)delta<-2 else delta<-1
if(controlOne>0)delta<-1
while(i<=nsam){
id<-colnames(bb.chr)[i]
paired.id<-colnames(bb.chr)[i+delta-1]
if(i+delta-1>nsam)stop("Check your data. Are all samples paired?")
if(controlOne>0)paired.id<-colnames(bb.chr)[sam.col+controlOne-1]
tag<-getHets(baf=bb.chr[,id],paired.baf=bb.chr[,paired.id],thr=thr.hets)
pp.bb<-bb.chr[,3]
pp.ll<-ll.chr[,3]
bb<-bb.chr[,id]
ll<-ll.chr[,id]
ll.paired<-ll.chr[,paired.id]
if(id==paired.id)A<-0 else A<-0
Nt<-length(tag)
kk<-1
while(kk<Nt){
ed<-kk+bin-1
if(ed>Nt)ed<-Nt
vv<-tag[kk:ed]
BAF.mean<-getBAFmean(bb[vv])
if(data.type=='copy')logR.mean<-log2(median(ll[vv]/ll.paired[vv]^A, na.rm=TRUE))-1
if(data.type=='log')logR.mean<-median(ll[vv]-ll.paired[vv]*A,na.rm=TRUE)
sam.seg<-cbind(id,chr,pp.bb[vv[1]],pp.bb[vv[length(vv)]],logR.mean,bin,BAF.mean,bin)
dat.chr<-rbind(dat.chr,sam.seg)
kk<-ed+1
cat('.')
}
i<-i+delta
if(i>nsam)break
cat('\ndone!\n')
}
return(na.omit(dat.chr))
}
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