R/AllClasses.R

In acidgenomics/r-chromium: 10X Genomics Chromium

#' Cell Ranger RNA-seq data set
#'
#' Contains UMI droplet-based single-cell RNA-seq data.
#'
#' @author Michael Steinbaugh
#' @export
#'
#' @examples
#' showClass("CellRanger")
setClass(
    Class = "CellRanger",
    contains = "SingleCellExperiment"
)
setValidity(
    Class = "CellRanger",
    method = function(object) {
        colData <- colData(object)
        metadata <- metadata(object)
        sampleData <- sampleData(object)
        ## Assays --------------------------------------------------------------
        ok <- validate(isSubset("counts", names(assays(object))))
        if (!isTRUE(ok)) {
            return(ok)
        }
        ## Row data ------------------------------------------------------------
        ok <- validate(
            is(rowRanges(object), "GenomicRanges"),
            is(rowData(object), "DataFrame")
        )
        if (!isTRUE(ok)) {
            return(ok)
        }
        ## Column data ---------------------------------------------------------
        ok <- validate(
            ## Require that metrics columns are defined.
            isSubset(metricsCols, colnames(colData)),
            ## Ensure that `interestingGroups` isn't slotted in colData.
            areDisjointSets("interestingGroups", colnames(colData))
        )
        if (!isTRUE(ok)) {
            return(ok)
        }
        ## Metadata ------------------------------------------------------------
        ok <- validateClasses(
            object = metadata,
            expected = list(
                "allSamples" = "logical",
                "call" = "call",
                "dir" = "character",
                "date" = "Date",
                "ensemblRelease" = "integer",
                "genomeBuild" = "character",
                "gffFile" = "character",
                "interestingGroups" = "character",
                "lanes" = "integer",
                "level" = "character",
                "matrixFiles" = "character",
                "organism" = "character",
                "packageVersion" = "package_version",
                "pipeline" = "character",
                "refJson" = "list",
                "refdataDir" = "character",
                "sampleDirs" = "character",
                "sampleMetadataFile" = "character",
                # > "sessionInfo" = "sessionInfo",
                "umiType" = "character",
                "wd" = "character"
            ),
            subset = TRUE
        )
        if (!isTRUE(ok)) {
            return(ok)
        }
        ok <- validate(
            !isSubset("sampleName", names(metadata)),
            isSubset(metadata[["level"]], c("genes", "transcripts"))
        )
        if (!isTRUE(ok)) {
            return(ok)
        }
        TRUE
    }
)