Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/methyAnalysis.R
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)
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DMRInfo |
A GRanges object or a list of GRanges objects (sigDMRInfo and sigDataInfo), which is the return of |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | 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')
}
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