Usage
featureFilter(eset, require.entrez=FALSE,
require.GOBP=FALSE, require.GOCC=FALSE,
require.GOMF=FALSE, exclude.ChrX=FALSE,
require.closeToTSS=FALSE, range.DistToTSS=c(-500, 300),
require.CpGisland=FALSE, ...)Arguments
eset
A MethyLumiSet or MethyLumiM object.
require.entrez
If TRUE, filter out features without an Entrez
Gene ID annotation.
require.GOBP, require.GOCC, require.GOMF
If TRUE,
filter out features whose target genes are not annotated to at least
one GO term in BP, CC and MF ontology, respectively.
exclude.ChrX
If TRUE, filter out features in chromosome
X to avoid gender effect.
require.closeToTSS
If TRUE, filter out features that
are not close to transcription start site (TSS). Features without
annotation of distance to TSS will also be removed. Can only used
for GoldenGate platform.
range.DistToTSS
Ignored if require.colseToTSS is
FALSE. A vector of numeric values of length 2, indicating the
range of tolerable distance from transcription start site (TSS) in
basepair (bp). If
require.clostToTSS is TRUE, features whose distance
to TSS falls outside this designated range will be removed. The
default value is $c(-500, 300)$, where $-500$ represents the
distance to TSS from the left and 300 the distance from the right.
require.CpGisland
If TRUE, filter out features that are not in
CpG islands.
...
Unused, but available for specializing methods.