mut_cn_to_pyclone: Parse mutation and CN input, creating a master table of...

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

Parse mutation and CN input, creating a master table of PyClone(VI) input Format: mutation_id, sample_id, ref_counts, alt_counts, normal_cn, major_cn, minor_cn, tumour_content mutation_id is a unique ID (position-based) sample_id is sample ref/alt_counts are read counts at Mutation, VAF the variant allele frequency mut_rdata is master_consensus_shared from somatic_n-of-1 workflow For somatic_n-of-1 workflow, CN is based on FACETS inputs

Description

Parse mutation and CN input, creating a master table of PyClone(VI) input Format: mutation_id, sample_id, ref_counts, alt_counts, normal_cn, major_cn, minor_cn, tumour_content mutation_id is a unique ID (position-based) sample_id is sample ref/alt_counts are read counts at Mutation, VAF the variant allele frequency mut_rdata is master_consensus_shared from somatic_n-of-1 workflow For somatic_n-of-1 workflow, CN is based on FACETS inputs

Usage

mut_cn_to_pyclone(mut_gr, cn_pattern, pp_pattern, tag)

Arguments

mut_gr	gr_master_consensus_all
cn_pattern	pattern matching FACETS input (fit_cncf_jointsegs.tsv)
pp_pattern	pattern matching FACETS polidy/purity (fit_ploidy_purity.tsv)

Value

none, writes a tsv for input to pyclone(VI)

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