countFeatures: countFeatures

In ETHZ-INS/diffUTR: diffUTR: Streamlining differential exon and 3' UTR usage

countFeatures

Description

countFeatures

Usage

countFeatures(
  bamfiles,
  bins,
  strandSpecific = 0,
  readLength = 50L,
  allowMultiOverlap = TRUE,
  inclNormalized = TRUE,
  tmpDir = tempdir(),
  ...
)

Arguments

bamfiles	A vector of paths to bam files
bins	A GRanges of bins in which to count reads (or path to a rds file containing such an object
strandSpecific	Passed to 'Rsubread::featureCounts'
readLength	Used as a minimum width to estimate read density.
allowMultiOverlap	Passed to 'Rsubread::featureCounts'
inclNormalized	Logical; whether to include normalized assays (needed for plotting)
tmpDir	Passed to 'Rsubread::featureCounts'
...	Passed to 'Rsubread::featureCounts'

Value

A RangedSummarizedExperiment-class

Examples

data("example_gene_annotation", package="diffUTR")
bins <- prepareBins(example_gene_annotation)
bam_files <- list.files(system.file("extdata", package="diffUTR"),
                        pattern="bam$", full=TRUE)
# not run
# se <- countFeatures(bam_files, bins, verbose=FALSE)

ETHZ-INS/diffUTR documentation built on March 18, 2023, 8:54 a.m.