countFeatures {diffUTR} | R Documentation

## 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)
    se <- countFeatures(bam_files, bins, verbose=FALSE)
    se

[Package diffUTR version 1.0.0 Index]