R/getGenotypesTable.R

In scoreInvHap: Get inversion status in predefined regions

#' Get genotypes table
#'
#' Get a matrix with the sample genotypes from all SNP.
#'
#' @param geno SnpMatrix (from plink format)
#' @param allele Data.frame with the alleles per SNP (from getAlleleTable)
#' @return Character matrix with the samples genotypes
getGenotypesTable <- function(geno, allele){
    names <- rownames(geno)

    ## Convert matrix of genotypes to numeric (0, 1, 2). Add 1 to match column indeces of allele table.
    geno <- methods::as(geno, "numeric") + 1
    geno[is.na(geno)] <- 4
    geno <- vapply(1:ncol(geno), function(x) unlist(allele[x, geno[,x], drop = TRUE]),
                   character(nrow(geno)))
    if (is.null(dim(geno))){
        geno <- matrix(geno, nrow = 1)
    }
    colnames(geno) <- rownames(allele)
    rownames(geno) <- names
    geno
}