haploMask: Mask haplogroup specific variants using haplogrep

In trichelab/MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

Note: this requires haplogrep, an external dependency.

Usage

haploMask(
  mvr,
  fasta.output = NULL,
  mask = TRUE,
  return.haplogroup = TRUE,
  ties = c("depth", "weight"),
  override = FALSE,
  java.path = NULL
)

Arguments

mvr	Input should be either an MVRanges or MVRangesList
fasta.output	Path to a location to output the per-sample consensus variant fasta files
mask	Whether to mask out the haplogroup specific SNPs
return.haplogroup	Return the inferred haplogroup
ties	Whether to use depth or weight to resolve variants to pass for haplogroup inference
override	This will override the java check and proceed even if a java install isn't detected
java.path	This is an option to specify a path to a java install (e.g. /usr/bin/java)

Value

An MVRanges or MVRangesList of masked haplogroup-specific variants

trichelab/MTseeker documentation built on March 8, 2021, 6:20 p.m.