Mercurial > repos > artbio > snvtocnv

comparison segmentation_sequenza.R @ 1:d2833cfb3f08 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
author artbio
date Thu, 19 May 2022 20:35:24 +0000
parents b77d7a0a45e8
children
comparison
equal deleted inserted replaced
0:b77d7a0a45e8 1:d2833cfb3f08
38 38
39 39
40 ## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22 40 ## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22
41 message(sprintf("\nExtraction step for %s", data_file)) 41 message(sprintf("\nExtraction step for %s", data_file))
42 42
43 chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", 43 chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
44 "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", 44 "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
45 "chr18", "chr19", "chr20", "chr21", "chr22") 45 "chr18", "chr19", "chr20", "chr21", "chr22", "chrX")
46 46
47 Sys.setenv(TZDIR = "/usr/share/zoneinfo/") 47 Sys.setenv(TZDIR = "/usr/share/zoneinfo/")
48 Sys.setenv(TZ = "US/Eastern") 48 Sys.setenv(TZ = "US/Eastern")
49 options(tz = "US/Eastern") 49 options(tz = "US/Eastern")
50 Sys.timezone(location = TRUE) 50 Sys.timezone(location = TRUE)