show ChIP-chip data aligned over genome features, e.g. TSSs

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Description

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

Usage

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

Arguments

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

Value

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

Author(s)

Joern Toedling

See Also

features2Probes, qop-class

Examples

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  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))

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