quantilesOverPositions {Ringo} | R Documentation

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

### Description

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

### Usage

    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

      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))

[Package Ringo version 1.42.1 Index]