genio (version 1.0.9)

read_plink: Read genotype and sample data in a plink BED/BIM/FAM file set.

Description

This function reads a genotype matrix (X) and its associated locus (bim) and individual (fam) data tables in the three plink files in BED, BIM, and FAM formats, respectively. All inputs must exist or an error is thrown. This function is a wrapper around the more basic functions read_bed, read_bim, read_fam. Below suppose there are \(m\) loci and \(n\) individuals.

Usage

read_plink(file, verbose = TRUE)

Arguments

file

Input file path, without extensions (each of .bed, .bim, .fam extensions will be added automatically as needed). Alternatively, input file path may have .bed extension (but not .bim, .fam, or other extensions).

verbose

If TRUE (default) function reports the paths of the files being read (after autocompleting the extensions).

Value

A named list with items in this order: X (genotype matrix), bim (tibble), fam (tibble). X has row and column names corresponding to the id values of the bim and fam tibbles.

See Also

read_bed, read_bim, read_fam.

Plink BED/BIM/FAM format reference: https://www.cog-genomics.org/plink/1.9/formats

Examples

# NOT RUN {
# first get path to BED file
file <- system.file("extdata", 'sample.bed', package = "genio", mustWork = TRUE)

# read genotypes and annotation tables
plink_data <- read_plink(file)
# genotypes
plink_data$X
# locus annotations
plink_data$bim
# individual annotations
plink_data$fam

# the same works without .bed extension
file <- sub('\\.bed$', '', file) # remove extension
# it works!
plink_data <- read_plink(file)

# }