make_pairtree_input: Write output for pairtree based on mutations in master TSV...

In brucemoran/somenone: R functions required by the somenone NextFlow nf-core pipeline

Write output for pairtree based on mutations in master TSV input

Description

Format: id, name, var_reads, total_reads, var_read_prob id is sequential s0..sn name is ID for the variant (chr:pos_ref>alt_HGVS) the below are comma-sep var_reads is reads supporting variant at variant locus total_reads is all reads at variant locus var_read_prob is based on CNA at locus; mutation at diploid locus is 0.5; in a duplicated (n=3) locus, 1/3 etc.

Usage

make_pairtree_input(
  rdata_input,
  cn_master,
  cn_pattern,
  pp_pattern,
  which_genome,
  tag
)

Arguments

rdata_input	is RData from process vcfGra including master_all, and gr_master_consensus_all
cn_master	master CNA from fctscon process in Nextflow pipeline)
cn_pattern	pattern matching FACETS input (fit_cncf_jointsegs.tsv)
pp_pattern	pattern matching FACETS ploidy/purity (fit_ploidy_purity.tsv)
which_genome	is GRCh37 or GRCh38
tag	is string to tag output

Value

none, writes a tsv for input to pairtree

brucemoran/somenone documentation built on Nov. 1, 2022, 3:56 p.m.