create.summary: create.summary

In mskilab/casereport: casereport: Whole-genome + transcription based report for cancer genomes

create.summary

Description

calculate stuff for summary table

Usage

create.summary(
  jabba_rds,
  snv_vcf,
  indel_vcf,
  verbose = FALSE,
  chrs = c(as.character(1:22), "X", "Y"),
  amp.thresh = 4,
  del.thresh = 0.5
)

Arguments

jabba_rds	(character) jabba rds
snv_vcf	(character) path to snv vcf/bcf
indel_vcf	(character) path to indel vcf/bcf
verbose	(logical) default FALSE
chrs	(character vector) seqnames default 1:22, x, y
amp.thresh	(numeric) default 4
del.thresh	(numeric) default 0.5

Value

list with names - purity - ploidy - junction_burden - del_mbp - amp_mbp - cna_mbp - cna_frac - mut_count - mut_per_mbp

mskilab/casereport documentation built on Oct. 19, 2022, 3 a.m.