annotateDMRInfo: Annotate the DMR (Differentially Methylated Region)
In methyAnalysis: DNA methylation data analysis and visualization

Description Usage Arguments Details Value Author(s) See Also Examples

Annotate the DMR (Differentially Methylated Region) information

1	annotateDMRInfo(DMRInfo, annotationDatabase, CpGInfo = NULL, flankRange = 500, promoterRange = 2000, EntrezDB = "org.Hs.eg.db", as.GRanges = TRUE)

`DMRInfo`	A GRanges object or a list of GRanges objects (sigDMRInfo and sigDataInfo), which is the return of `identifySigDMR`
`annotationDatabase`	Annotation database: a TxDb package, TxDb object or GRanges object.
`CpGInfo`	A Bed file or GRanges object, which keeps the CpG-island information
`flankRange`	The flank range to be added to the input GRanges object
`promoterRange`	Define the size of promoter range at the upstream of TSS. User can also directly provide the GRanges object
`EntrezDB`	The Entrez database for mapping from Entrez ID to gene symbols
`as.GRanges`	Whether return a GRanges object or a data.frame

This function is to annotate the DMRs to the gene promoters or bodies. The annotation information is attached as additional columns of the GRanges object values.

Return a GRanges object or list of GRanges when the as.GRanges is TRUE. Or else it returns a data.frame or a list of data.frame objects (sigDMRInfo and sigDataInfo). The annotation information is attached as additional columns of the GRanges object values or the data.frame.

Pan Du

See Also annotateGRanges

	data(exampleMethyGenoSet)
	## get sample type information
	sampleType <- colData(exampleMethyGenoSet)$SampleType
	
	## Do differential test
	allResult <- detectDMR.slideWin(exampleMethyGenoSet, sampleType=sampleType, testMethod='ttest')

	## Identify the DMR (Differentially Methylated Region) by setting proper parameters.
	## Here we just use default ones
	allDMRInfo <- identifySigDMR(allResult)

	## Annotate significant DMR info
	if (require(TxDb.Hsapiens.UCSC.hg19.knownGene)) {
		DMRInfo.ann <- annotateDMRInfo(allDMRInfo, 'TxDb.Hsapiens.UCSC.hg19.knownGene')
	}