featureFilter {methylumi} | R Documentation |
Features with insufficient annotation
carry little value for the subsequent data analysis. The function
featureFilter
provides options of filtering features (CpG
sites) from a MethyLumiSet
(or MethyLumiM
) object based
on available annotation data.
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, ...)
eset |
A |
require.entrez |
If |
require.GOBP, require.GOCC, require.GOMF |
If |
exclude.ChrX |
If |
require.closeToTSS |
If |
range.DistToTSS |
Ignored if |
require.CpGisland |
If |
... |
Unused, but available for specializing methods. |
The function featureFilter
returns a list consisting of:
eset |
The filtered |
filter.log |
A list giving details of how many probe sets where removed for each annotation-based filtering step performed. |
Chao-Jen Wong cwon2@fhcrc.org
R. Bourgon, R. Gentleman, W. Huber, Independent filtering increases power for detecting differentially expressed genes, PNAS, vol. 107, no. 21, pp:9546-9551.