plotVcfPercNa: Plot VCF

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Plot VCF

Description

Plot markers from a VCF file along chromosomes, colored according to their percentage of missing genotypes.

Usage

plotVcfPercNa(
  vcf.file,
  yieldSize = NA_integer_,
  dict.file = NULL,
  seq.id = NULL,
  seq.start = NULL,
  seq.end = NULL,
  main = "Density of missing genotypes",
  plot.it = TRUE
)

Arguments

vcf.file	path to the VCF file (if the bgzip index doesn't exist in the same directory, it will be created)
yieldSize	number of records to yield each time the file is read from (see ?TabixFile) if seq.id is NULL
dict.file	path to the SAM dict file (see https://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary) if seq.id is specified with no start/end
seq.id	sequence identifier to work on (e.g. "chr2")
seq.start	start of the sequence to work on (if NULL, whole seq)
seq.end	end of the sequence to work on (if NULL, whole seq)
main	main title of the plot
plot.it	if TRUE, autoplot from the ggbio package will be used

Value

GenomicRange

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.