Permalink
Browse files

fixed corrected_copy_number for combined titan and ichor results

  • Loading branch information...
gavinha committed Oct 10, 2018
1 parent 7dfeaa9 commit a5ad26f5b11e49e697bb9c9bda249aeda8c5ae94
Showing with 4 additions and 3 deletions.
  1. +3 −2 TitanCNA.snakefile
  2. +1 −1 code/combineTITAN-ichor.R
@@ -138,10 +138,11 @@ rule copyOptSolution:
"logs/titan/optSolution/copyOptSolution.log"
shell:
"""
curDir=`pwd`
for i in `cut -f11 {input} | grep -v "path"`;
do
echo -e "Copying results for ${{i}} to {output}"
cp -r ${{i}}* {output}
echo -e "Creating sym links for $curDir/${{i}} to {output}"
ln -s ${{curDir}}/${{i}}* {output}
done
"""

@@ -78,7 +78,7 @@ ichor.cn <- cbind(Sample = id, ichor.cn)
#ichor.cn[, CopyNumber := state - 1]
ichor.cn[, Position := start]
setnames(ichor.cn, c("chr", "start", paste0(id,".copy.number"), paste0(id,".event"), paste0(id,".logR"), "end"),
c("Chr", "Start", "Copy_Number", "TITANcall", "LogRatio", "End"))
c("Chr", "Start", "CopyNumber", "TITANcall", "LogRatio", "End"))


## get chromosome style

0 comments on commit a5ad26f

Please sign in to comment.