enrichmentCalc {Repitools} | R Documentation |
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 |
seq.len |
If sequencing reads need to be extended, the fragment size to be used. |
verbose |
Whether to print the progress of processing. |
... |
Argument |
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.frame
s.
Aaron Statham
require(GenomicRanges) data(samplesList) # Loads 'samples.list.subset'. seqlengths(samples.list.subset) tc <- enrichmentCalc(samples.list.subset, seq.len = 300)