rnb.execute.snp.removal {RnBeads} | R Documentation |
Removes all probes overlapping with single nucleotide polymorphisms (SNPs) from the given dataset.
rnb.execute.snp.removal(rnb.set, snp = rnb.getOption("filtering.snp"))
rnb.set |
Methylation dataset as an object of type inheriting |
snp |
Criterion for the removal of sites or probes based on overlap with SNPs. Possible values are
|
list
of four elements:
"dataset.before"
Copy of rnb.set
.
"dataset"
The (possibly) modified dataset object after removing probes that overlap with SNPs.
"filtered"
integer
vector storing the indices (in beta matrix of the unfiltered
dataset) of all removed sites or probes.
"snp"
The value of the snp
parameter.
Yassen Assenov
library(RnBeads.hg19) data(small.example.object) rnb.set.filtered <- rnb.execute.snp.removal(rnb.set.example, "any")$dataset identical(meth(rnb.set.example), meth(rnb.set.filtered)) # FALSE