R/mat2strata.R

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

#' Define strata based on rows of a matrix
#'
#' Use the rows of a matrix to define a set of strata for a stratified permutation test
#'
#' @param mat A covariate matrix, as individuals x covariates
#'
#' @return A vector of character strings: for each row of `mat`,
#' we use [base::paste()] with `collapse="|"`.
#'
#' @examples
#' iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
#'
#' Xcovar <- get_x_covar(iron)
#' perm_strata <- mat2strata(Xcovar)
#'
#' @seealso [get_x_covar()], [scan1perm()]
#' @export
mat2strata <-
    function(mat)
{
    if(is.null(mat)) return(NULL)
    if(!is.matrix(mat) && is.data.frame(mat)) mat <- as.matrix(mat)
    if(!is.matrix(mat)) stop("mat should be a matrix")

    result <- apply(mat, 1, paste, collapse="|")
    names(result) <- rownames(mat)

    result
}