Import SNP genotypes — read_snp

This function reads in SNP genotypes 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), and remaining columns are the samples. First column is expected to be the locus identity (e.g. SNP identifier), and remaining columns are the samples. The genotypes are expected to be encoded as "AA", "AB", "BA" or "BB".

Usage

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

Arguments

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

Value

A data frame of genotype values ("AA", "AB", "BA" or "BB"). Each row is for a locus. The locus identity is indicated in the first column and named snp. Remaining columns are samples.