getGeneInfo: getGeneInfo to extract geneInfo slot from MEE.data or Pair...

In lijingya/ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

getGeneInfo is a function to easily extract geneInfo out of a MEE.data or Pair object. By specifying geneID or symbol, geneInfo for the defined genes (geneID or symbol) will be extracted out of MEE.data or Pair object. When range is specified, the geneInfo falling into the range will be extracted.

Usage

getGeneInfo(object, geneID, symbol, range)

## S4 method for signature 'ANY'
getGeneInfo(object, geneID, symbol, range)

Arguments

object	MEE.data or Pair object
geneID	A vector of genes' id. When specified, only these gene coordinates will be output.
symbol	A vector of genes' symbols . When specified, only these gene coordinates will be output.
range	A GRanges object. When specified, only the geneInfo locating within these loci will be output.

Value

Gene annotation information such as gene id, symbol and coordinates.

Author(s)

Lijing Yao (maintainer: [e-mail])

Examples

geneInfo <- txs()
mee <- fetch.mee(geneInfo=geneInfo)
Genes <- getGeneInfo(mee, geneID = "55811")
Genes <- getGeneInfo(mee, symbol ="ADCY10")
Genes <- getGeneInfo(mee, range = GRanges(seqnames="chr1", ranges=IRanges(1000000,1600000)))

lijingya/ELMER documentation built on May 21, 2019, 6:14 a.m.