R/WriteTsv.R

In daskelly/earlycross: Extensions to Seurat

#' Write raw data in tab-separated data format
#'
#' @param obj Seurat object to print
#' @param outfile Character. Name of a tsv file that should be written to
#' @param raw A logical scalar. Should raw data be written?
#' @param gzip A logical scalar. Should data be gzipped after writing?
#' @export
#' @importFrom assertthat assert_that
#' @importFrom data.table fwrite
#' @examples
#' WriteTsv(obj, filename, raw=FALSE)
WriteTsv <- function(obj, outfile, raw = TRUE, gzip = TRUE) {
    assert_that(class(obj) == "seurat")

    if (raw) {
        mat <- obj@raw.data[, obj@cell.names] %>%
            as.matrix()
    } else {
        mat <- obj@data[, obj@cell.names] %>%
            as.matrix()
    }
    cat("gene\t", paste(colnames(mat), collapse = "\t"), "\n", file = outfile)
    fwrite(as.data.frame(mat), file = outfile, append = TRUE, quote = FALSE, sep = "\t",
        row.names = TRUE, col.names = FALSE)
    if (gzip)
        gzip(outfile)
    return()
}