rnb.execute.low.coverage.masking {RnBeads} | R Documentation |
Replaces all low coverage sites by NA
.
rnb.execute.low.coverage.masking( rnb.set, covg.threshold = rnb.getOption("filtering.coverage.threshold") )
rnb.set |
Methylation dataset as an object of type inheriting |
covg.threshold |
Threshold for minimal acceptable coverage, given as a non-negative |
List of three elements:
"dataset.before"
Copy of rnb.set
.
"dataset"
The (possibly) modified dataset after retaining sites on autosomes only.
"mask"
A logical matrix of dimension meth(rnb.set,type="sites")
indicating which
methylation values have been masked
Fabian Mueller