annotateGRanges {methyAnalysis} | R Documentation

## Annotate a GRanges object

### Description

Annotate a GRanges object based on a transcription database

### Usage

    annotateGRanges(grange, annotationDatabase, CpGInfo = NULL, exons = FALSE, flankRange = 0, promoterRange = 2000, checkGeneBody = FALSE, EntrezDB = "org.Hs.eg.db")

### Arguments

`grange` | A GRanges object
`annotationDatabase` | Annotation database: a TxDb package, TxDb object or GRanges object.
`CpGInfo` | A Bed file or GRanges object, which keeps the CpG-island information
`exons` | Whether to annotate at the exon level. exons can be either TRUE/FALSE or a GRanges object represent the exon annotation.
`flankRange` | The flank range to be added to the input GRanges object
`promoterRange` | Define the size of promoter range at the upstream of TSS. Users can also directly provide the GRanges object
`checkGeneBody` | Determine whether to check the overlapping with gene body or just check the promoter region
`EntrezDB` | The Entrez database for mapping from Entrez ID to gene symbols

### Details

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

### Value

Return an annotated GRanges object with the annotation information attached as additional columns.

### Author(s)

Pan Du

### See Also

See Also `annotateDMRInfo`

### Examples

    	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)
    	sigDMRInfo <- allDMRInfo$sigDMRInfo
    	class(sigDMRInfo)

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

[Package methyAnalysis version 1.28.0 Index]