enrichmentCalc {Repitools}R Documentation

Calculate sequencing enrichment

Description

Function to calculate enrichment over the whole genome of sequencing reads.

Usage

  ## S4 method for signature 'GRanges'
enrichmentCalc(x, seq.len = NULL, verbose = TRUE)
  ## S4 method for signature 'GRangesList'
enrichmentCalc(x, verbose = TRUE, ...)

Arguments

x

A GRangesList or GRanges object. All chromosome lengths must be stored in the Seqinfo of this object.

seq.len

If sequencing reads need to be extended, the fragment size to be used.

verbose

Whether to print the progress of processing.

...

Argument seq.len above, not directly used in the GRangesList method.

Details

If seq.len is supplied, x is firstly extended, and then turned into a coverage object. The number of extended reads covering each base pair of the genome is then tabulated, and returned as a data.frame.

Value

For the GRanges method, data.frame containing columns coverage and bases. For the GRangesList method, a list of such data.frames.

Author(s)

Aaron Statham

Examples

  require(GenomicRanges)
  data(samplesList)  # Loads 'samples.list.subset'.
  seqlengths(samples.list.subset)

  tc <- enrichmentCalc(samples.list.subset, seq.len = 300)
[Package Repitools version 1.26.0 Index]