computeDatasetSignature {PREDA} | R Documentation

## Function to compute dataset signature for recurrent significant genomic regions

### Description

Function to compute dataset signature for recurrent significant genomic regions

### Usage

    # computeDatasetSignature(.Object, genomicRegionsList=genomicRegionsList,
    # multTestCorrection="fdr", signature_qval_threshold=0.05,
    # returnRegions=TRUE, use.referencePositions=TRUE)

    computeDatasetSignature(.Object, ...)

### Arguments

`.Object` | Object of class GenomicAnnotationsForPREDA
`...` | See below genomicRegionsList: List of genomicRegions objects for which the recurrent overlapping regions will be evaluated multTestCorrection: Multiple testing correction that will be adopted to correct the statistic p-values. Possible values are "fdr", for benjamini and Hochberg multiple testing correction and "qvalue" for p-values correction performed with qvalue package. signature_qval_threshold: Threshold used to select significant regions resulting from the dataset signature statistic returnRegions: Logical, if TRUE (default) the genomic regions constituting the daaset signature are returned, otherwise a PREDAresults object containing dataset signature statistics is returned. use.referencePositions: Logical, if TRUE the input reference positions used for PREDA analysis wil be used to identify significant genomic regions boundaries as well.

### Details

The function adopts a binomial test to identify significant recurrence of genomic regions across multiple dataset sampels.

### Value

A GenomicRegions object (if returnRegions = TRUE) or a PREDAresults object containing dataset signature statistics (if returnRegions = FALSE)

### Author(s)

Francesco Ferrari

### See Also

`GenomicRegions`, `PREDAResults`

### Examples

     ## 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)

[Package PREDA version 1.38.0 Index]