bed2matrix: Convert a bed to a matrix

In pcadapt: Fast Principal Component Analysis for Outlier Detection

Convert a bed to a matrix

Description

Convert a bed to a matrix

Usage

bed2matrix(bedfile, n = NULL, p = NULL)

Arguments

bedfile	Path to a bed file.
n	Number of samples. Default reads it from corresponding fam file.
p	Number of SNPs. Default reads it from corresponding bim file.

Value

An integer matrix.

Examples

bedfile <- system.file("extdata", "geno3pops.bed", package = "pcadapt")
mat <- bed2matrix(bedfile)
dim(mat)
table(mat)

pcadapt documentation built on Aug. 29, 2023, 5:07 p.m.