Nothing
ibdhap.reduce.states <-
function(qibd.filename, dat.filename, output.filename){
#glean information from the par file
par.file<-read.table(dat.filename, fill =TRUE, colClasses = "numeric")
n.snps<- par.file[3,1] #number of markers
n.sets<-par.file[2,1] #number of set of haplotypes
temp<-FALSE
for( iset in 1:n.sets){
#make the text above the (sets of) marker information in both files the same
line1<-scan(qibd.filename, skip=((n.snps+2)*(iset-1)), nlines=1, what='raw')
write(line1, file=output.filename, ncolumns=length(line1), append=temp)
temp<-TRUE
line2<-scan(qibd.filename, skip=((n.snps+2)*(iset-1)+1), nlines=1, what='raw')
write(line2, file=output.filename, ncolumns=length(line2), append=TRUE)
rm(line1,line2)
#read the qibd.filename, just the information for the markers in "iset"
ibd.dat<-scan(qibd.filename,what = "numeric",skip = (2*(iset)+(n.snps)*(iset-1)), nlines = n.snps)
ibd.dat<-t(matrix(as.numeric(unlist(ibd.dat)), nrow=17))
reduced.dat <- t( apply(ibd.dat,1,sumcol) )
reduced.dat <- cbind( ibd.dat[,1:2], reduced.dat)
write.table( reduced.dat,file=output.filename, append = TRUE, col.names=FALSE, row.names=FALSE)
}
return(paste("file", output.filename, "written in", getwd()) )
}
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