filter.snpeff: filter.snpeff

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

filter.snpeff

Description

Overlaps annotated VCF with genes provided in delimited file and returns results as data.table If VCF doesn't exist or is not provided returns an empty data.table

Usage

## S3 method for class 'snpeff'
filter(
  vcf,
  gngt.fname,
  onc,
  tsg,
  drivers.fname,
  ref.name = "hg19",
  verbose = FALSE,
  type = NULL
)

Arguments

vcf	(character) vcf file name
gngt.fname	(character) gencode gTrack file name
onc	(character) path to .rds file with character vector of oncogenes
tsg	(character) path to .rds file with character vector of TSGs
ref.name	(character) one of hg19 or hg38
verbose	(logical) default FALSE

Value

data.table with columns gene, seqnames, pos, REF, ALT, variant.p, vartype, annotation

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