Filter: Filter VCF files

In nspope/r2vcftools: An R interface for vcftools

Description

Given a "vcfLink" object, removes loci/samples corresponding to a set of filtering options.

Usage

Filter(object, ...)

## S4 method for signature 'vcfLink'
Filter(object, arguments = filterOptions(),
  indels = c("keep", "remove", "only"), verbose = TRUE)

filterOptions(min.meanDP = NULL, max.meanDP = NULL, minDP = NULL,
  maxDP = NULL, min.alleles = NULL, max.alleles = NULL, maf = NULL,
  max.maf = NULL, minQ = NULL, max.missing = NULL, hwe = NULL,
  thin = NULL)

Arguments

object	an object of class "vcfLink"
arguments	optional arguments for vcftools as returned by filterOptions, see vcftools manual.
indels	what to do with indels; "keep" leaves them in, "remove" removes them, and "only" discards everything but indels.
verbose	print stdout from vcftools?

nspope/r2vcftools documentation built on Oct. 10, 2019, 2:06 a.m.