Skip to contents

Calculate Coverage Profiles

Source: R/coverage.r
coverage.Rd

coverage() calculates the coverage profiles for loci specified by the user, using data from BAM files.

Usage

coverage(
  data,
  subsettingBams = FALSE,
  coverageType = "average",
  verbose = TRUE,
  featureCountsOtherParams = list()
)

Arguments

data

The List object returned by newExperiment().

subsettingBams

A Logical. Determines whether the BAM files should be subset by the loci specified by the user. This can significantly improve computation time.

coverageType

A String. Select how to compute the coverage profiles:

  • fivePrime : coverage profiles compute on 5' ends of reads ;

  • threePrime : coverage profiles compute on 3' ends of reads ;

  • average : coverageFactory coverage profile compute on average of 5' & 3' ends of reads ;

  • fullLength : coverage profiles compute on full length reads.

verbose

A Logical. Should all the operations performed be displayed ?

featureCountsOtherParams

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