Mercurial > repos > artbio > snvtocnv

diff segmentation_sequenza.R @ 2:9265faa93098 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8-dirty"
author artbio
date Fri, 19 Feb 2021 14:56:45 +0000
parents 0e54da14f831
children e299c477b475
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line diff
--- a/segmentation_sequenza.R	Thu Feb 18 19:03:54 2021 +0000
+++ b/segmentation_sequenza.R	Fri Feb 19 14:56:45 2021 +0000
@@ -42,9 +42,13 @@
 ## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22
 message(sprintf("\nExtraction step for %s", data_file))
 
+chrom_list = c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
+               "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
+               "chr18", "chr19", "chr20", "chr21", "chr22")
+
 segfile <- sequenza.extract(data_file,
-                            verbose = TRUE) # ,
-                            # chromosome.list = as.character(c(1:22)))
+                            verbose = TRUE,
+                            chromosome.list = chrom_list)
 
 ## Estimation of cellularity and ploidy