read_snp_genotypes: Import SNP genotypes

In maialab/daeqtlr: DAEQTL Mapping

Import SNP genotypes

Description

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.

maialab/daeqtlr documentation built on May 18, 2022, 6:53 a.m.