featureFilter {methylumi} | R Documentation

## Annotation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object

### Description

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.

### 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.

### Value

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.

### Author(s)

Chao-Jen Wong cwon2@fhcrc.org

### References

R. Bourgon, R. Gentleman, W. Huber, Independent filtering increases power for detecting differentially expressed genes, PNAS, vol. 107, no. 21, pp:9546-9551.

### See Also

`nsFilter`

[Package methylumi version 2.34.0 Index]