Import SNP genomic positions — read_snp_gen

This function reads in genomic positions from a text file. The data is expected to be in tabular format. First column is expected to be the locus identity (e.g. SNP identifier), second column is the human chromosome (e.g., 22 or X), and the third column is the position.

Usage

read_snp_gen_positions(file, sep = ",", header = TRUE, ...)

Arguments

file: A path to a file containing the SNP genomic positions.
sep: The separator between columns.
header: Does the first data line contain column names?
...: Extra arguments passed on to data.table::fread().

Value

A data frame of genomic positions. Each row is for a locus. The locus identity is indicated in the first column (snp). Second column is the chromosome, and the third column is the position.