grok_vcf: grok_vcf

In mskilab/skitools: Various mskilab R utilties

grok_vcf

Description

Does additional processing of annotated vcf output and produces a more readable granges output.

Warning: this function expects SnpEFF VCF input!!!

Usage

grok_vcf(
  x,
  label = NA,
  keep.modifier = TRUE,
  long = FALSE,
  oneliner = FALSE,
  verbose = FALSE
)

Arguments

x	GRanges input
label	character value that will be added as a $label column
keep.modifier	logical flag whether to keep modifier output
long	logical flag whether to expand output so that every annotation has its own row, warning: will create duplicate rows for a given variant
oneliner	logical flag whether to add a oneliner for the annotation
verbose	logical flag whether to pritn output

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.