Count Reads per Gene/Feature — bb_count

Counts reads overlapping genomic features. Uses GenomicAlignments::summarizeOverlaps() if available, otherwise shells out to featureCounts from the Subread package.

Usage

bb_count_reads(
  bam_paths,
  annotation,
  method = c("auto", "internal", "featureCounts"),
  threads = 4L,
  feature_type = "exon",
  attr_type = "gene_id",
  paired = FALSE
)

Arguments

bam_paths: Character vector. Paths to BAM files.
annotation: Character. Path to GTF/GFF annotation file.
method: Character. "auto" tries GenomicAlignments first, then featureCounts; "internal" forces GenomicAlignments; "featureCounts" forces the external tool.
threads: Integer. Number of threads for featureCounts. Default 4.
feature_type: Character. Feature type to count (GTF column 3). Default "exon".
attr_type: Character. Attribute to group by. Default "gene_id".
paired: Logical. Paired-end data. Default FALSE.

Value

A numeric matrix of counts (genes x samples). Rownames are gene IDs, colnames are derived from BAM file names.

Examples

# \donttest{
# Requires BAM files and a GTF annotation
# counts <- bb_count_reads(c("s1.bam", "s2.bam"), "genes.gtf")
# }