| findPeaksOnSmoothed {Ringo} | R Documentation |
Given an ExpressionSet of smoothed probe intensities, an environment with the mapping of probes to chromosomes, and a vector of thresholds for calling genomic sites enriched, this function finds the peaks consisting of enriched genomic positions, with probes mapped to them. 'Adjacent' enriched positions are condensed into a single peak.
findPeaksOnSmoothed(smoothedX, probeAnno, thresholds, allChr = c(1:19, "X", "Y"), distCutOff = 600, minProbesInRow = 3, cellType=NULL, verbose = TRUE)
smoothedX |
Object of class ExpressionSet holding the
smoothed probe intensities, e.g. the result of function
computeRunningMedians. |
probeAnno |
environment containing the probe to genome mapping |
thresholds |
numeric vector of threshold above which smoothed
probe intensities are considered to correspond to enriched
probes. The vector has to be of length equal the number of samples
in smoothedX, with a single threshold for each sample. |
allChr |
character vector of all chromosomes, on which peaks are
to be found. Every chromosome here has to have probes mapped to it
in the probeAnno environment. |
distCutOff |
integer; maximum amount of base pairs at which enriched probes are condensed into one peak. |
minProbesInRow |
integer; minimum number of enriched
probes required for a peak; see details for further
explanation. |
cellType |
character; name of cell type the data stems from,
maybe could be taken from pData(smoothedX) |
verbose |
logical; extended output to STDOUT? |
Specifying a minimum number of probes for a peak (argument
minProbesInRow) guarantees that a peak is supported by a
reasonable number of measurements in probe-sparse regions.
For example, if there's only one enriched probe within a certain
genomic 1kb region and no other probes can been mapped to that
region, this single probe does arguably not provide enough evidence
for calling this genomic region enriched.
A list of class peakList, holding objects of class peak
that were found on the supplied data.
Joern Toedling toedling@ebi.ac.uk
peakByThreshold,computeRunningMedians,
relatePeaks
exDir <- system.file("exData",package="Ringo")
load(file.path(exDir,"exampleProbeAnno.rda"))
load(file.path(exDir,"exampleX.rda"))
smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
modColumn = "Cy5", allChr = "9", winHalfSize = 400)
peaksX <- findPeaksOnSmoothed(smoothX, probeAnno=exProbeAnno,
thresholds=0.45, allChr="9", distCutOff=600, cellType="human")
if (interactive())
plot(peaksX[[1]], smoothX, probeAnno=exProbeAnno, gff=exGFF)
peaksX <- relatePeaks(peaksX, exGFF)
as.data.frame.peakList(peaksX)