quantilesOverPositions {Ringo} | R Documentation |
Function to show the ChIP-chip data aligned over certain genome features, for example transcription start sites (TSSs).
quantilesOverPositions(xSet, selGenes, g2p, positions = seq(-5000, 10000, by = 250), quantiles = c(0.1, 0.5, 0.9))
xSet |
an |
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
|
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
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))