Quantifying Region Expression — counting • DiffSegR

In brief, counting() quantify expression of regions found by segmenting the per-base Log2-FC of each locus.

In details counting() calls Rsubread::featureCounts() which assigns to the regions the mapped reads from each replicate of both the reference and the alternative biological condition. By default a read is allowed to be assigned to more than one region if it is found to overlap with more than one region. Rsubread::featureCounts() ends by building a count matrix. counting() then returns regions and associated count matrix as SummarizedExperiment object. Alternatively, users may opt to quantify the expression of each region directly from the coverage profiles.

Usage

counting(
  data,
  features,
  featureCountsType = "fromBam",
  featureCountsOtherParams = list(),
  verbose = TRUE
)

Arguments

data

The List object returned by newExperiment().

features

A GRanges object that contains the segment boundaries (returned by segmentationLFC()).

featureCountsType

A String. Select how to summarize counts:

fromBam : from bam files using Rsubread::featureCounts ;
fromCoverage : from coverage profiles.

featureCountsOtherParams

A List. Other paramters passed on to Rsubread::featureCounts().

verbose

A Boolean. Should all the operations performed be displayed ?