Mercurial > repos > artbio > mutational_patterns

comparison mutational_patterns.R @ 5:fe31d059a482 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 8726066cfb70109de05cbdb7aa7c08ee11b957e9"
author artbio
date Tue, 06 Oct 2020 13:33:44 +0000
parents 7ba08c826888
children 2c1d58f5c296
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4:7ba08c826888 5:fe31d059a482
100 parser$addData(json_dict) 100 parser$addData(json_dict)
101 fileslist <- parser$getObject() 101 fileslist <- parser$getObject()
102 vcf_paths <- attr(fileslist, "names") 102 vcf_paths <- attr(fileslist, "names")
103 element_identifiers <- unname(unlist(fileslist)) 103 element_identifiers <- unname(unlist(fileslist))
104 ref_genome <- opt$genome 104 ref_genome <- opt$genome
105 vcf_table <- data.frame(element_identifier=element_identifiers, path=vcf_paths) 105 vcf_table <- data.frame(element_identifier=as.character(element_identifiers), path=vcf_paths)
106 106
107 library(MutationalPatterns) 107 library(MutationalPatterns)
108 library(ref_genome, character.only = TRUE) 108 library(ref_genome, character.only = TRUE)
109 library(ggplot2) 109 library(ggplot2)
110 110