computeDatasetSignature {PREDA} | R Documentation |
Function to compute dataset signature for recurrent significant genomic regions
# computeDatasetSignature(.Object, genomicRegionsList=genomicRegionsList, # multTestCorrection="fdr", signature_qval_threshold=0.05, # returnRegions=TRUE, use.referencePositions=TRUE) computeDatasetSignature(.Object, ...)
.Object |
Object of class GenomicAnnotationsForPREDA |
... |
See below
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The function adopts a binomial test to identify significant recurrence of genomic regions across multiple dataset sampels.
A GenomicRegions object (if returnRegions = TRUE) or a PREDAresults object containing dataset signature statistics (if returnRegions = FALSE)
Francesco Ferrari
## Not run: require(PREDAsampledata) data(SODEGIRCNanalysisResults) data(GEDataForPREDA) SODEGIR_CN_GAIN<-PREDAResults2GenomicRegions( SODEGIRCNanalysisResults, qval.threshold=0.01, smoothStatistic.tail="upper", smoothStatistic.threshold=0.1) CNgain_signature<-computeDatasetSignature(GEDataForPREDA, genomicRegionsList=SODEGIR_CN_GAIN) ## End(Not run)