DataForPREDA-class      Class "DataForPREDA" is used to manage all of
                        the data required as input for PREDA analysis
DataForPREDA2GenomicAnnotationsForPREDA
                        extract a GenomicAnnotationsForPREDA object
                        from a data DataForPREDA object
DataForPREDA2StatisticsForPREDA
                        extract a StatisticsForPREDA object from a data
                        DataForPREDA object
DataForPREDA2dataframe
                        extract data and annotations as a dataframe
DataForPREDAMedianCenter
                        Function to scale median value of DataForPREDA
                        statistics to zero
GenomicAnnotations-class
                        Class "GenomicAnnotations" to manage
                        information about genomic features
GenomicAnnotations2GenomicAnnotationsForPREDA
                        generate a GenomicAnnotationsForPREDA object
                        from a GenomicAnnotations object
GenomicAnnotations2dataframe
                        extracts annotations as a dataframe
GenomicAnnotations2reference_positions
                        extract reference positions from the
                        GenomicAnnotations
GenomicAnnotationsExtract
                        extract optional annotations for a specific
                        region
GenomicAnnotationsFilter_neg
                        filter annotations to remove selected
                        chromosomes
GenomicAnnotationsFilter_pos
                        filter annotations to keep selected chromosomes
GenomicAnnotationsForPREDA-class
                        Class "GenomicAnnotationsForPREDA"
                        GenomicAnnotations class with additional slot
                        specifying the reference position for PREDA
                        analysis
GenomicAnnotationsForPREDA2GenomicAnnotations
                        extract the GenomicAnnotations object from the
                        GenomicAnnotationsForPREDA object
GenomicAnnotationsForPREDA2PREDAResults
                        add PREDA results information to genomic
                        annotatations creating a PREDAResults object
GenomicAnnotationsForPREDA2dataframe
                        extract annotations as a dataframe
GenomicAnnotationsForPREDAFromfile
                        Function to create a GenomicAnnotationsForPREDA
                        object from a txt file
GenomicAnnotationsFromLibrary
                        Function extracting a GenomicAnnotations object
                        from a Bioconductor annotation library
GenomicAnnotationsFromdataframe
                        Function to create a GenomiAnnotations object
                        from a dataframe
GenomicAnnotationsFromfile
                        Function to create a GenomiAnnotations object
                        from a text file
GenomicAnnotationsSortAndCleanNA
                        sort annotations according to selected
                        chromosomes and to remove genes containing any
                        NA annotation field
GenomicRegions-class    Class "GenomicRegions" is used to manage
                        information about genomic regions
GenomicRegions2dataframe
                        extract genomic regions information as a
                        dataframe object
GenomicRegionsAnnotate
                        extract annotations from a GenomicAnnotations
                        object for a set of regions specified as a
                        GenomicRegions object
GenomicRegionsChrNumber
                        determine the number of chromosomes with
                        genomic regions
GenomicRegionsComparison
                        compare GenomicRegions objects to identify
                        overlaps and differences
GenomicRegionsCreateRegionsIds
                        generate unique ids for GenomicRegions objects
GenomicRegionsFilter_neg
                        filter genomic regions to remove selected
                        chromosomes
GenomicRegionsFilter_pos
                        filter genomic regions to keep selected
                        chromosomes
GenomicRegionsFindOverlap
                        Function to find overlap between GenomicRegions
                        objects
GenomicRegionsFromdataframe
                        Function to create a GenomiRegions object from
                        a dataframe
GenomicRegionsFromfile
                        Function to create a GenomiRegions object from
                        a text file
GenomicRegionsNumber    determine the number of genomic regions
GenomicRegionsSpan      determine the span of each genomic region
GenomicRegionsTotalSpan
                        determine the total span of genomic regions
MergeStatisticAnnotations2DataForPREDA
                        Merge a StatisticsForPREDA and a
                        GenomicAnnotationsForPREDA object into a
                        DataForPREDA object.
PREDADataAndResults-class
                        Class "PREDADataAndResults" is used to manage
                        the PREDA analysis output
PREDADataAndResults2dataframe
                        extract data and annotations as a dataframe
                        with probeids as rownames
PREDAResults-class      Class "PREDAResults" ~is used to manage the
                        PREDA analysis output
PREDAResults2GenomicRegions
                        identify significant genomic regions from a
                        PREDAResults object
PREDAResults2GenomicRegionsSingle
                        identify significant genomic regions from a
                        single analysis in a PREDAResults object
PREDAResults2PREDADataAndResults
                        merge PREDAResults and input statistics to
                        create a PREDADataAndResults object
PREDAResults2dataframe
                        extact preda results statistics as a data frame
                        object
PREDAResultsGetObservedFlags
                        extract genomic positions with significant
                        alterations as a matrix of flags from a
                        PREDAResults object
PREDA_main              function performing the core of PREDA analysis
SODEGIR_GEstatistics    Wrapper function for gene expression statistics
                        preprocessing for SODEGIR analysis
SODEGIRpreprocessingGE
                        Wrapper function for gene expression data
                        preprocessing for SODEGIR analysis
StatisticsForPREDA-class
                        Class "StatisticsForPREDA" is used to manage
                        the datamatrix containing statistics for PREDA
                        analyses
StatisticsForPREDA2dataframe
                        extract data as a dataframe with probeids as
                        rownames
StatisticsForPREDAFilterColumns_neg
                        filter statistics to remove selected analyses
StatisticsForPREDAFilterColumns_pos
                        filter statistics to keep selected analyses
StatisticsForPREDAFromdataframe
                        Function to create a StatisticsForPREDA objet
                        from a dataframe
StatisticsForPREDAFromfile
                        Function to create a StatisticsForPREDA objet
                        from a txt file
analysesNames           Get the names of the analyses in the from PREDA
                        objects
computeDatasetSignature
                        Function to compute dataset signature for
                        recurrent significant genomic regions
eset2GenomicAnnotations
                        Function building a GenomicAnnotations object
                        on an ExpressionSet object
genomePlot              draw a genome plot
getStatisticByName      extract data for individual analyses using the
                        analysis name
preprocessingGE         Wrapper function for gene expression data
                        preprocessing for differential expression
                        analysis with PREDA
statisticsForPREDAfromEset
                        function to compute a statisticsForPREDA object
                        from an ExpressionSet object
