Annotation-based filtering of features (CpG sites) in a MethyLumiSet or MethyLumiM object

Features with insufficient annotation carry little value for subsequent data analysis. The function `featureFilter` provides options for 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 the BP, CC and MF ontology, respectively.
exclude.ChrX: If `TRUE`, filter out features on chromosome X to avoid gender effects.
require.closeToTSS: If `TRUE`, filter out features that are not close to a transcription start site (TSS). Features without an annotation of distance to TSS will also be removed. Can only be used for the GoldenGate platform.
range.DistToTSS: Ignored if `require.closeToTSS` is `FALSE`. A numeric vector of length 2 indicating the range of tolerable distance from the transcription start site (TSS) in basepairs. Features whose distance to TSS falls outside this range will be removed. The default is \(c(-500, 300)\), where \(-500\) is 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

A list consisting of:

eset: The filtered `MethyLumiSet` or `MethyLumiM` object.
filter.log: A list giving details of how many probe sets were removed for each annotation-based filtering step performed.

References

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

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