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 = c("8"), winHalfSize = 400, combineReplicates=TRUE) peaksX <- findPeaksOnSmoothed(smoothX, probeAnno=exProbeAnno, thresholds=1.5, allChr = c("8"),distCutOff=600, cellType="HL1") if (interactive()) plot(peaksX[[2]], smoothX, probeAnno=exProbeAnno, gff=exGFF) peaksX <- relatePeaks(peaksX, exGFF) as.data.frame.peakList(peaksX)