ELMER (version 1.4.2)

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

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)
"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.

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)))