quantilesOverPositions: show ChIP-chip data aligned over genome features, e.g. TSSs
In Ringo: R Investigation of ChIP-chip Oligoarrays

Description Usage Arguments Value Author(s) See Also Examples

Function to show the ChIP-chip data aligned over certain genome features, for example transcription start sites (TSSs).

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quantilesOverPositions(xSet, selGenes, g2p,
                       positions = seq(-5000, 10000, by = 250),
                       quantiles = c(0.1, 0.5, 0.9))

`xSet`	an `ExpressionSet` holding the ChIP-chip data
`selGenes`	character; vector of genome features, e.g. transcripts, to use for the plot
`g2p`	A list object containing the mapping between genome positions and probes on the microarray. Created with the function `features2Probes`.
`positions`	Numeric vector of positions related to the coordinates of the genome features, such as in which distances of the TSS the values should be computed over the aligned data
`quantiles`	numeric; which quantiles to compute over the aligned data

An object of class qop, which can be visualized by its plot method.

Joern Toedling

features2Probes, qop-class

  ringoExampleDir <- system.file("exData",package="Ringo")
  load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
  trans2Probe <- features2Probes(exGFF, exProbeAnno)
  load(file.path(ringoExampleDir,"exampleX.rda"))
  exampleSX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
     modColumn = "Cy5", allChr = "9", winHalfSize = 400)
  exampleC <- findChersOnSmoothed(exampleSX, probeAnno=exProbeAnno,
     thresholds=0.2, allChr="9", distCutOff=600, cellType="human")
  exampleC <- relateChers(exampleC, exGFF)
  exampleQop <- quantilesOverPositions(exampleSX,
     selGenes=getFeats(exampleC), quantiles=c(0.5, 0.9),
     g2p=trans2Probe, positions=seq(-4000, 1000, by=250))
  show(exampleQop)
  plot(exampleQop, ylim=c(-0.5, 2.1))