Create a genotype matrix — get

This function takes genotype data in PLINK format as input and returns a geno data frame, which can be passed to map_qtl using the geno argument. See the package vignette for details.

get_geno(candidate, chromosomes, plink.prefix, plink.suffix)

Arguments

candidate: A data frame containing feature IDs and SNP IDs. The first column must contain feature IDs and the second column must contain SNP IDs.
chromosomes: An integer vector specifying chromosomes.
plink.prefix: A character string specifying the prefix of PLINK files.
plink.suffix: A character string specifying the suffix of PLINK files.

Value

A data frame formatted as input for MatrixEQTL. The first column contains SNP IDs. The rest of the columns contain genotypes coded as (0, 1, 2). Each column corresponds to each sample.

Examples

if (FALSE) { # \dontrun{
candidate <- data.frame(feat_id = "f1", snp_id = "g1")
geno <- get_geno(
    candidate = candidate,
    chromosomes = 1,
    plink.prefix = "path/to/plink",
    plink.suffix = "bed"
)
} # }