R/loadOctadCounts.R

In Bin-Chen-Lab/OCTAD: Open Cancer TherApeutic Discovery (OCTAD)

#' @export
#' @import rhdf5
#' @importFrom octad.db get_ExperimentHub_data
#' @importFrom utils write.csv data txtProgressBar read.csv2 head read.csv
#' @importFrom grDevices pdf
#### runsRGES #######
loadOctadCounts <- function(sample_vector = NULL, type = "tpm", file = NULL) {
    if (missing(sample_vector)) {
        stop("sample_vector input not found")
    }

    if (is.null(file)) {
        stop("h5 file with counts not provided")
    }

    transcripts <- as.character(rhdf5::h5read(file, "meta/transcripts"))
    samples <- as.character(rhdf5::h5read(file, "meta/samples"))
    if (type == "counts") {
        message("loading", length(transcripts), "log2 expression values for", length(sample_vector), "samples",
            sep = " ")
        exprData <- rhdf5::h5read(file, "data/count", index = list(seq_len(length(transcripts)), which(samples %in%
            sample_vector)))
        rownames(exprData) <- transcripts
        colnames(exprData) <- samples[samples %in% sample_vector]
        rhdf5::H5close()
        return(exprData)
    } else if (type == "tpm") {
        message("loading", length(transcripts), "TPM expression values for", length(sample_vector), "samples",
            sep = " ")
        exprData <- rhdf5::h5read(file, "data/tpm", index = list(seq_len(length(transcripts)), which(samples %in%
            sample_vector)))
        rownames(exprData) <- transcripts
        colnames(exprData) <- samples[samples %in% sample_vector]
        rhdf5::H5close()
        return(exprData)
    } else {
        message("Some parameters are missing, check everything is ok and restart function")
    }
    rhdf5::H5close()
}