getProbeInfo: getProbeInfo to extract probeInfo slot from MEE.data or Pair...

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

Description

getProbeInfo is a function to easily extract probeInfo out of a MEE.data or Pair object. By specifying probe, probeInfo for the defined set of probes will be extracted out of MEE.data or Pair object. Option chr will restrain the output probeInfo to certain chromosomes. When range is specified, the probeInfo falling into the range will be extracted.

Usage

getProbeInfo(object, chr, probe, range)

## S4 method for signature 'ANY'
getProbeInfo(object, chr, probe, range)

Arguments

object	MEE.data or Pair object
chr	A vector of chromosome such chr1, chr2. When specified, only the probeInfo locating on these chromosome will be output.
probe	A vector of probes' name. When specified, only these probes' coordinate will be output.
range	A GRanges object. When specified, only probeInfo locating within these loci will be output.

Value

Probe information such as names, coordinates.

Author(s)

Lijing Yao (maintainer: [e-mail])

Examples

probeInfo <- GRanges(seqnames = c("chr1","chr1","chr3"),
ranges = IRanges(start = c(1,6,20),end = c(2,7,21)),
name=c("cg1","cg2","cg3"))
mee <- fetch.mee(probeInfo=probeInfo)
Probes <- getProbeInfo(mee,chr="chr1") # get probes which locate on the chr1
Probes <- getProbeInfo(mee, probe = "cg1") # get certain probes information
Probes <- getProbeInfo(mee, range = GRanges(seqnames="chr1", ranges=IRanges(5,20)))

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