computeDatasetSignature: Function to compute dataset signature for recurrent...

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Function to compute dataset signature for recurrent significant genomic regions

Usage

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# 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

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 ## 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)

PREDA documentation built on May 6, 2019, 2:07 a.m.