importVCF: importVCF

In GenomicTools.fileHandler: File Handlers for Genomic Data Analysis

Description

Import a VCF function

Usage

importVCF(file, na.seq = "./.")

Arguments

file	The file name
na.seq	The missing value definition

Details

This function imports a VCF file.

In case the logicl flag 'phased' is set to TRUE then the genotypes are expected to be in the format 0|0, otherwise they are expected to be like 0/1 .

The example file was downloaded from here:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/exon/snps/

Value

A vcf object

Author(s)

Daniel Fischer

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.vcf", package="GenomicTools.fileHandler")
 # Import the example vcf file  
   importVCF(fpath)

GenomicTools.fileHandler documentation built on March 26, 2020, 7:23 p.m.