R/get-markers.R

In churchill-lab/qtl2api: QTL2 API Library

#' Get the markers (more for API benefits).  Not for qtl2.
#'
#' @param chrom The chromosome to filter on.
#'
#' @return A tibble with the following columns: marker_id, chr, bp
#' @export
get_markers <- function(chrom = NULL) {
    ret <- markers %>%
        janitor::clean_names() %>%
        dplyr::filter(!is.na(.data$pos)) %>%
        dplyr::select(
            marker_id = .data$marker_id,
            chr       = .data$chr,
            pos       = .data$pos
        )

    if (all(ret$pos < 1000)) {
        # convert from Mbp to bp
        ret$pos <-  as.integer(ret$pos * 1000000)
    }

    if (!is.null(chrom)) {
        ret %<>% dplyr::filter(.data$chr == chrom)
    }

    ret
}