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 |