old_dir <- getwd()
setwd(tempdir())
data(hapRes)
data(simu)
namesL <- simu[["namesL"]]
haploN <- simu[["haploN"]]
snvs <- simu[["snvs"]]
annot <- simu[["annot"]]
alleleIimp <- simu[["alleleIimp"]]
write.table(namesL,file="dataSim1fabia_individuals.txt",
quote = FALSE,row.names = FALSE,col.names = FALSE)
write(as.integer(haploN),file="dataSim1fabia_annot.txt",
ncolumns=100)
write(as.integer(snvs),file="dataSim1fabia_annot.txt",
append=TRUE,ncolumns=100)
write.table(annot,file="dataSim1fabia_annot.txt",
sep = " ", quote = FALSE,row.names = FALSE,
col.names = FALSE,append=TRUE)
write(as.integer(haploN),file="dataSim1fabia_mat.txt",
ncolumns=100)
write(as.integer(snvs),file="dataSim1fabia_mat.txt",
append=TRUE,ncolumns=100)
for (i in 1:haploN) {
a1 <- which(alleleIimp[i,]>0.01)
al <- length(a1)
b1 <- alleleIimp[i,a1]
a1 <- a1 - 1
dim(a1) <- c(1,al)
b1 <- format(as.double(b1),nsmall=1)
dim(b1) <- c(1,al)
write.table(al,file="dataSim1fabia_mat.txt",
sep = " ", quote = FALSE,row.names = FALSE,
col.names = FALSE,append=TRUE)
write.table(a1,file="dataSim1fabia_mat.txt",
sep = " ", quote = FALSE,row.names = FALSE,
col.names = FALSE,append=TRUE)
write.table(b1,file="dataSim1fabia_mat.txt",
sep = " ", quote = FALSE,row.names = FALSE,
col.names = FALSE,append=TRUE)
}
mergedIBDsegmentList <- hapRes$mergedIBDsegmentList
individuals <- individuals(mergedIBDsegmentList[[1]])
tagSNVs <- tagSNVs(mergedIBDsegmentList[[1]])
tagSNVs <-
as.integer(sort.int(as.integer(unique(tagSNVs))))
tagSNVPositions <-
tagSNVPositions(mergedIBDsegmentList[[1]])
labelIndividuals <-
labelIndividuals(mergedIBDsegmentList[[1]])
Lout <- readSamplesSpfabia(X="dataSim1fabia_mat",
samples=individuals,lowerB=0,upperB=1000.0)
tagSNVsL <- list(tagSNVs)
labelsK <- c("model L")
plotIBDsegment(Lout=Lout,tagSNV=tagSNVsL,
physPos=tagSNVPositions,colRamp=12,val=c(0.0,2.0,1.0),
chrom="1",count=0,labelsNA=labelIndividuals,
labelsNA1=labelsK)
setwd(old_dir)
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