featureFilter: Annotation-based Filtering of Features (CpG sites) in a...
In seandavi/methylumi: Handle Illumina methylation data

Description Usage Arguments Value Author(s) References See Also

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 `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.

The function featureFilter returns a list consisting of:

`eset`	The filtered `MethyLumiSet` or `MethyLumiM` object.
`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.

nsFilter

seandavi/methylumi documentation built on Oct. 28, 2021, 12:42 a.m.