PREDA (version 1.18.0)

computeDatasetSignature: 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.

Value

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

Details

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

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)