enrichmentCalc: Calculate sequencing enrichment
In Repitools: Epigenomic tools

Description Usage Arguments Details Value Author(s) Examples

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

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

`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.

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.

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

Aaron Statham

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

  tc <- enrichmentCalc(samples.list.subset, seq.len = 300)