getCoverage {MOCHA}

Get sample-specific coverage files for each sample-cell population.

Description

getCoverage takes the output of MOCHA::getPopFrags and returns a GRanges of singe-basepair resolution coverage.

Usage

getCoverage(
  popFrags,
  normFactor,
  TxDb,
  cl,
  filterEmpty = FALSE,
  verbose = FALSE
)

Arguments

popFrags

GRangesList of fragments for all sample/cell populations

normFactor

Normalization factor. Can be either be one, in which case all coverage files will be normalized by the same value, or the same length as the GRangesList

TxDb

The TxDb-class transcript annotation package for your organism (e.g. "TxDb.Hsapiens.UCSC.hg38.refGene"). This must be installed. See Bioconductor AnnotationData Packages.

cl

cl argument to pblapply

filterEmpty

True/False flag on whether or not to carry forward regions without coverage.

verbose

Boolean variable to determine verbosity of output.

Value

popCounts A GRangesList of coverage for each sample and cell population