Mercurial > repos > artbio > mutational_patterns
comparison mutational_patterns.R @ 5:fe31d059a482 draft
"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 |