test/test_oncoprint.R
In jokergoo/cotools: R functions
files1 = scan(pipe("ls /icgc/dkfzlsdf/analysis/hipo/hipo_047/results_per_pid_pcawg/*/mpileup/*_somatic_functional_snvs_conf_8_to_10.vcf"), what = "character")
samples = gsub("^.*results_per_pid_pcawg/(.*?)/mpileup.*$", "\\1", files1)
snv_oncoprint(files1, samples)
files2 = scan(pipe("ls /icgc/dkfzlsdf/analysis/hipo/hipo_047/results_per_pid_pcawg/*/platypus_indel/*_somatic_functional_indels_conf_8_to_10.vcf"), what = "character")
samples = gsub("^.*results_per_pid_pcawg/(.*?)/platypus_indel.*$", "\\1", files2)
indel_oncoprint(files2, samples)
snv_indel_oncoprint(files1, files2, samples)
jokergoo/cotools documentation built on May 19, 2019, 6:24 p.m.
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files1 = scan(pipe("ls /icgc/dkfzlsdf/analysis/hipo/hipo_047/results_per_pid_pcawg/*/mpileup/*_somatic_functional_snvs_conf_8_to_10.vcf"), what = "character")
samples = gsub("^.*results_per_pid_pcawg/(.*?)/mpileup.*$", "\\1", files1)
snv_oncoprint(files1, samples)
files2 = scan(pipe("ls /icgc/dkfzlsdf/analysis/hipo/hipo_047/results_per_pid_pcawg/*/platypus_indel/*_somatic_functional_indels_conf_8_to_10.vcf"), what = "character")
samples = gsub("^.*results_per_pid_pcawg/(.*?)/platypus_indel.*$", "\\1", files2)
indel_oncoprint(files2, samples)
snv_indel_oncoprint(files1, files2, samples)
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