R/featureCoverage.R

In scmeth: Functions to conduct quality control analysis in methylation data

#' Coverage based on the genomic feature
#'
#'Provides Coverage metrics for the sample by each genomic features provided
#'by the user
#'@param bs bsseq object
#'@param features list of genomic features, e.g. genes_exons, genes_introns,
#'cpg_islands, cpg_shelves
#'Names are based on the annotatr packages, so all the features provided by the
#'annotatr
#'package will be supported in this function
#'@param genomebuild reference alignment, i.e. mm10 or hg38
#'@return a data frame with genomic feature names and the number of
#'CpG covered in each feature
#'@examples
#'directory <- system.file("extdata/bismark_data", package='scmeth')
#'bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
#'featureCoverage(bs, c('cpg_islands', 'cpg_shores'), 'hg38')
#'@importFrom DelayedArray rowSums
#'@importFrom GenomeInfoDb seqlevelsStyle
#'@importFrom annotatr builtin_genomes
#'@importFrom annotatr build_annotations
#'@importFrom annotatr annotate_regions
#'@importFrom annotatr summarize_annotations
#'@import GenomicRanges
#'@export


featureCoverage <- function(bs, features, genomebuild){

    annotationFeatures <- c()
    for (i in features){
    annotationFeatures <- c(paste0(genomebuild, '_', i), annotationFeatures)
    }

    annots_gr = annotatr::build_annotations(genome = genomebuild,
                                        annotations = annotationFeatures)
    GenomeInfoDb::seqlevelsStyle(bs) <- "UCSC"
    nSamples <- dim(bs)[2]

    sumAnnotMatrix <- matrix(nrow=length(features), ncol=nSamples)
    featureLabel <- rep(NA, length(features))
    for (i in seq_len(nSamples)){
        bsCell <- bs[,i]

        # CpGs that are observed
        coverageMatrix <- getCoverage(bsCell)
        ind <- DelayedArray::rowSums(coverageMatrix)>0
        # Intersect the regions with the reference annotations

        dm_annotated = annotatr::annotate_regions(
            regions = GenomicRanges::granges(bsCell)[ind,],
            annotations = annots_gr,
            ignore.strand = TRUE,
            quiet = TRUE)
        sumAnnot <- annotatr::summarize_annotations(dm_annotated, quiet=TRUE)
        sumAnnotMatrix[,i] <- sumAnnot$n[match(annotationFeatures, sumAnnot$annot.type)]/sum(ind)
        featureLabel[1:length(sumAnnot$annot.type)] <- sumAnnot$annot.type
    }
    colnames(sumAnnotMatrix) <- colnames(bs)
    rownames(sumAnnotMatrix) <- features

    return(sumAnnotMatrix)
}