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