R/DataInput.R

In gscreend: Analysis of pooled genetic screens

#' Create PoolScreenExp Experiment
#'
#' @param data Input data object containing gRNA level data
#' (SummarizedExperiment)
#'
#' @return object  PoolScreenExp object
#' @export
#'
#' @examples raw_counts <- read.table(
#'                         system.file('extdata', 'simulated_counts.txt',
#'                         package = 'gscreend'),
#'                         header=TRUE)
#'
#'counts_matrix <- cbind(raw_counts$library0, raw_counts$R0_0, raw_counts$R1_0)
#'
#'rowData <- data.frame(sgRNA_id = raw_counts$sgrna_id,
#'gene = raw_counts$Gene)
#'
#'colData <- data.frame(samplename = c('library', 'R1', 'R2'),
#'timepoint = c('T0', 'T1', 'T1'))
#'
#'library(SummarizedExperiment)
#'se <- SummarizedExperiment(assays=list(counts=counts_matrix),
#'rowData=rowData, colData=colData)
#'
#'# create a PoolScreenExp experiment
#'pse <- createPoolScreenExp(se)
#'
#' @importFrom methods is
createPoolScreenExp <- function(data) {
    if (is(data, "SummarizedExperiment")) {
        message(
            "Creating PoolScreenExp object from a SummarizedExperiment object."
            )
        object <- createPoolScreenExpFromSE(data)
        object
    } else {
        stop(
            "Error: input data is not of the suported input format: ",
            "SummarizedExperiment.")
    }
}

#' Create PoolScreenExp Experiment from summarized experiment
#'
#' @param data SummarizedExperiment object containing gRNA level data
#'
#' @return object
#'
#' @importFrom methods new
#' @keywords internal
createPoolScreenExpFromSE <- function(data) {
    object <- new("PoolScreenExp")

    # Check whether reference and sample are named correctly
    checksum_ref <- sum(data$timepoint == "T0")
    checksum_sample <- sum(data$timepoint == "T1")
    if (checksum_ref != 1) {
        stop("gscreend is currently only implemented",
                "for usage of one reference (T0). ",
                "You are using ", checksum_ref, " references.")
    } else if (checksum_sample < 1) {
        stop("There is no sample T1.")
    } else if (checksum_sample + checksum_ref !=  length(data$timepoint)) {
        stop("Timepoints can be named T0 or T1 only. ",
                "One or more of your timepoints is names differently.")
    } else {message("References and samples are named correctly.")}

    # Check whether rownames are correct
    if (!is.element("sgRNA_id", colnames(rowData(data)))) {
        stop("The rowData of SummarizedExperiment needs to contain a column named \"sgRNA_id\". ",
             "The columns you provided are: ", paste(colnames(rowData(data)), " "))
    } else if (!is.element("gene", colnames(rowData(data)))) {
        stop("The rowData of SummarizedExperiment needs to contain a column named \"gene\". ",
             "The columns you provided are: ", paste(colnames(rowData(data)), " "))
    }
    else {message("Data concerning sgRNA and genes is provided.")}

    sgRNAData(object) <- data
    FittingOptions(object) <- list(IntervalFraction = 0.1)
    object
}