Read a PLINK .bed file of BED-encoded local ancestry calls

Source: R/ancestry_split.R

Reads a PLINK binary genotype file (.bed/.bim/.fam trio) into an integer matrix, for the case where local ancestry has been encoded as PLINK genotype calls at ancestry-tract "SNPs" (as consumed by src/step1_vcf_split_by_ancestry.R): homozygous first allele = pure EUR/EUR (code 1), heterozygous = mixed AFR/EUR (code 2), homozygous second allele = pure AFR/AFR (code 3), missing = no call (code 0). This matches snpStats::read.plink()'s raw numeric convention (values feed directly into split_diploid/ancestry_split_dosage as pt_matrix/ancestry without snpStats as a dependency.

read_bed_file(bed, bim, fam)

Arguments

bed

Path to the .bed file.

bim

Path to the .bim file (variant IDs are taken from column 2).

fam

Path to the .fam file (sample IDs are taken from column 2, i.e. IID).

Value

Integer matrix (variants x samples), dimnamed from the .bim/.fam files. Values: 0 = no call, 1 = homozygous first allele, 2 = heterozygous, 3 = homozygous second allele.

Examples

ext <- system.file("extdata", package = "lantern")
pt <- read_bed_file(file.path(ext, "toy_ancestry.bed"),
                    file.path(ext, "toy_ancestry.bim"),
                    file.path(ext, "toy_ancestry.fam"))
pt[, 1:6]   # ancestry tracts x samples, codes 1/2/3
#>                         S001 S002 S003 S004 S005 S006
#> chr19:1000000-4999999      3    3    3    3    2    2
#> chr19:5000000-8999999      3    2    3    2    3    3
#> chr19:10000000-13999999    3    3    3    3    3    3
#> chr19:15000000-18999999    3    3    2    3    3    3
#> chr19:30000000-33999999    1    3    2    2    3    2
#> chr19:35000000-38999999    3    2    2    3    2    2
#> chr19:40000000-43999999    2    2    2    2    2    3
#> chr19:45000000-48999999    3    3    2    3    3    3