Import SNP zygosity — read_snp

This function reads in SNP zygosity levels 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. The genotypes are expected to be encoded as "hom" or "het", for homozygous and heterozygous, respectively.

Usage

read_snp_zygosity(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 zygosity levels: "hom" for homozygous or "het"for heterozygous. Each row is for a locus. The locus identity is indicated in the first column and named snp. Remaining columns are samples.