R/subsetBy.R

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

#' Subset by support across samples
#'
#' A convienient wrapper around calcSupport and subset.
#'
#' @param object RangedSummarizedExperiment: CAGE data quantified at CTSS,
#'   cluster or gene-level.
#' @param inputAssay character: Name of assay holding input expression values.
#' @param outputColumn character: Name of column in rowRanges to hold support
#'   values.
#' @param unexpressed numeric: Support will be calculated based on features
#'   larger than this cutoff.
#' @param minSamples numeric: Only features with support in more than this
#'   number of samples will be kept.
#'
#' @return RangedSummarizedExperiment with support added as a column in
#'   rowRanges and features with less support than minSamples removed.
#'
#' @family Subsetting functions
#' @family Calculation functions
#'
#' @importClassesFrom Matrix dgCMatrix
#' @export
#' @examples
#' data(exampleBidirectional)
#'
#' # Keep clusters with at least one tag in two samples
#' subsetBySupport(exampleBidirectional)
#'
#' # Keep clusters with at least two tags in four samples
#' subsetBySupport(exampleBidirectional, unexpressed=1, minSamples=2)
subsetBySupport <- function(object, inputAssay = "counts", outputColumn = "support", 
    unexpressed = 0, minSamples = 1) {
    # Pre-checks
    assert_that(is.numeric(minSamples))
    
    # Call function
    message("Calculating support...")
    object <- calcSupport(object = object, inputAssay = inputAssay, outputColumn = outputColumn, 
        unexpressed = unexpressed)
    before <- nrow(object)
    
    # Subset
    message("Subsetting...")
    object <- object[rowData(object)[, outputColumn] > minSamples, ]
    after <- nrow(object)
    removed <- before - after
    
    # Print some info
    message("Removed ", removed, " out of ", before, " regions (", round(removed/before * 
        100, digits = 1), "%)")
    
    # Return
    object
}

#' Subset by composition across samples
#'
#' A convenient wrapper around calcComposition and subset.
#'
#' @param object RangedSummarizedExperiment: CAGE data quantified at CTSS,
#'   cluster or gene-level.
#' @param inputAssay character: Name of assay holding input expression values.
#' @param outputColumn character: Name of column in rowRanges to hold
#'   composition values.
#' @param unexpressed numeric: Composition will be calculated based on features
#'   larger than this cutoff.
#' @param genes character: Name of column in rowData holding genes (NAs are not
#'   allowed.)
#' @param minSamples numeric: Only features with composition in more than this
#'   number of samples will be kept.
#'
#' @return RangedSummarizedExperiment with composition values added as a column
#'   in rowData and features with less composition than minSamples removed.
#' @family Subsetting functions
#' @family Calculation functions
#'
#' @export
#' @examples
#' data(exampleUnidirectional)
#'
#' # Annotate clusters with geneIDs:
#' library(TxDb.Mmusculus.UCSC.mm9.knownGene)
#' txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
#'
#' exampleUnidirectional <- assignGeneID(exampleUnidirectional,
#'                                       geneModels=txdb,
#'                                       outputColumn='geneID')
#' exampleUnidirectional <- subset(exampleUnidirectional, !is.na(geneID))
#'
#' # Keep only clusters more than 10% in more than one sample:
#' calcComposition(exampleUnidirectional)
#'
#' # Keep only clusters more than 5% in more than 2 samples:
#' subsetByComposition(exampleUnidirectional, unexpressed = 0.05, minSamples=2)
subsetByComposition <- function(object, inputAssay = "counts", outputColumn = "composition", 
    unexpressed = 0.1, genes = "geneID", minSamples = 1) {
    # Pre-checks
    assert_that(is.numeric(minSamples))
    
    # Call function
    message("Calculating composition...")
    object <- calcComposition(object = object, inputAssay = inputAssay, outputColumn = outputColumn, 
        unexpressed = unexpressed, genes = genes)
    before <- nrow(object)
    
    # Subset
    message("Subsetting...")
    object <- object[rowData(object)[, outputColumn] > minSamples, ]
    after <- nrow(object)
    removed <- before - after
    
    # Print some info
    message("Removed ", removed, " out of ", before, " regions (", round(removed/before * 
        100, digits = 1), "%)")
    
    # Return
    object
}