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.frame`s.

### 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 1.32.0 Index]