# Position Related Data Analysis

## Documentation for package ‘PREDA’ version 1.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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