read_vcf: Read a VCF file into R session

In PMBio/cardelino: Clone Identification from Single Cell Data

Read a VCF file into R session

Description

Read a VCF file into R session

Usage

read_vcf(
  vcf_file,
  genome = "GRCh37",
  seq_levels_style = "Ensembl",
  verbose = TRUE
)

Arguments

vcf_file	character(1), path to VCF file to read into R session as a CollapsedVCF object
genome	character(1), string indicating the genome build used in the VCF file(s) (default: "GRCh37")
seq_levels_style	character(1), string passed to seqlevelsStyle the style to use for chromosome/contig names (default: "Ensembl")
verbose	logical(1), should messages be printed as function runs?

Value

a vcf object

Examples

vcf <- read_vcf(system.file("extdata", "cells.donorid.vcf.gz",
               package = "cardelino"))

PMBio/cardelino documentation built on Nov. 21, 2022, 4:52 a.m.