grab_vcf: read in a (possibly gzipped) VCF file and return it as a data...

In eriqande/snps2assays: Prepare SNP Assay Orders from ddRAD or RAD Loci

Description

This scans a VCF file to find the header line (by searching for a line starting with "#CHROM"), and then it reads it in and returns it as a data frame. It doesn' worry about the formatting of the genotype columns because we are typically concerned here just with getting CHROM, POS, REF, and ALT. In fact, by default, those four columns are all that this function returns

Usage

grab_vcf(path, all_cols = FALSE, top_test = 200)

Arguments

path	The path to a VCF file (which may or may not be gzipped)
all_cols	Logical indicating whether to return all columns (TRUE) or only CHROM, POS, REF, and ALT.
top_test	How many lines to scan from the top of the file to look for the "#CHROM" showing that it is the header.

Examples

grab_vcf(system.file("textdata", "vcf.txt.gz", package = "snps2assays"))

eriqande/snps2assays documentation built on Oct. 9, 2020, 5:22 p.m.