read_vcf: Read a VCF file into R session

Description Usage Arguments Value Examples

View source: R/read_data.R

Description

Read a VCF file into R session

Usage

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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

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

davismcc/cardelino documentation built on Aug. 21, 2019, 3:31 p.m.