PREDA: Position RElated Data Anlysis

Package for the position related analysis of quantitative functional genomics data.

AuthorFrancesco Ferrari <francesco.ferrari@unimore.it>
Date of publicationNone
MaintainerFrancesco Ferrari <francesco.ferrari@unimore.it>
LicenseGPL-2
Version1.20.0

View on Bioconductor

Man pages

analysesNames: Get the names of the analyses in the from PREDA objects

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

DataForPREDA2dataframe: extract data and annotations as a dataframe

DataForPREDA2GenomicAnnotationsForPREDA: extract a GenomicAnnotationsForPREDA object from a data...

DataForPREDA2StatisticsForPREDA: extract a StatisticsForPREDA object from a data DataForPREDA...

DataForPREDA-class: Class "DataForPREDA" is used to manage all of the data...

DataForPREDAMedianCenter: Function to scale median value of DataForPREDA statistics to...

eset2GenomicAnnotations: Function building a GenomicAnnotations object on an...

genomePlot: draw a genome plot

GenomicAnnotations2dataframe: extracts annotations as a dataframe

GenomicAnnotations2GenomicAnnotationsForPREDA: generate a GenomicAnnotationsForPREDA object from a...

GenomicAnnotations2reference_positions: extract reference positions from the GenomicAnnotations

GenomicAnnotations-class: Class "GenomicAnnotations" to manage information about...

GenomicAnnotationsExtract: extract optional annotations for a specific region

GenomicAnnotationsFilter_neg: filter annotations to remove selected chromosomes

GenomicAnnotationsFilter_pos: filter annotations to keep selected chromosomes

GenomicAnnotationsForPREDA2dataframe: extract annotations as a dataframe

GenomicAnnotationsForPREDA2GenomicAnnotations: extract the GenomicAnnotations object from the...

GenomicAnnotationsForPREDA2PREDAResults: add PREDA results information to genomic annotatations...

GenomicAnnotationsForPREDA-class: Class "GenomicAnnotationsForPREDA" GenomicAnnotations class...

GenomicAnnotationsForPREDAFromfile: Function to create a GenomicAnnotationsForPREDA object from a...

GenomicAnnotationsFromdataframe: Function to create a GenomiAnnotations object from a...

GenomicAnnotationsFromfile: Function to create a GenomiAnnotations object from a text...

GenomicAnnotationsFromLibrary: Function extracting a GenomicAnnotations object from a...

GenomicAnnotationsSortAndCleanNA: sort annotations according to selected chromosomes and to...

GenomicRegions2dataframe: extract genomic regions information as a dataframe object

GenomicRegionsAnnotate: extract annotations from a GenomicAnnotations object for a...

GenomicRegionsChrNumber: determine the number of chromosomes with genomic regions

GenomicRegions-class: Class "GenomicRegions" is used to manage information about...

GenomicRegionsComparison: compare GenomicRegions objects to identify overlaps and...

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

getStatisticByName: extract data for individual analyses using the analysis name

MergeStatisticAnnotations2DataForPREDA: Merge a StatisticsForPREDA and a GenomicAnnotationsForPREDA...

PREDADataAndResults2dataframe: extract data and annotations as a dataframe with probeids as...

PREDADataAndResults-class: Class "PREDADataAndResults" is used to manage the PREDA...

PREDA_main: function performing the core of PREDA analysis

PREDAResults2dataframe: extact preda results statistics as a data frame object

PREDAResults2GenomicRegions: identify significant genomic regions from a PREDAResults...

PREDAResults2GenomicRegionsSingle: identify significant genomic regions from a single analysis...

PREDAResults2PREDADataAndResults: merge PREDAResults and input statistics to create a...

PREDAResults-class: Class "PREDAResults" ~is used to manage the PREDA analysis...

PREDAResultsGetObservedFlags: extract genomic positions with significant alterations as a...

preprocessingGE: Wrapper function for gene expression data preprocessing for...

SODEGIR_GEstatistics: Wrapper function for gene expression statistics preprocessing...

SODEGIRpreprocessingGE: Wrapper function for gene expression data preprocessing for...

StatisticsForPREDA2dataframe: extract data as a dataframe with probeids as rownames

StatisticsForPREDA-class: Class "StatisticsForPREDA" is used to manage the datamatrix...

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...

statisticsForPREDAfromEset: function to compute a statisticsForPREDA object from an...

StatisticsForPREDAFromfile: Function to create a StatisticsForPREDA objet from a txt file

Functions

analysesNames Man page
analysesNames,PREDAResults-method Man page
analysesNames,StatisticsForPREDA-method Man page
computeDatasetSignature Man page
computeDatasetSignature,GenomicAnnotationsForPREDA-method Man page
DataForPREDA2dataframe Man page
DataForPREDA2dataframe,DataForPREDA-method Man page
DataForPREDA2GenomicAnnotationsForPREDA Man page
DataForPREDA2GenomicAnnotationsForPREDA,DataForPREDA-method Man page
DataForPREDA2StatisticsForPREDA Man page
DataForPREDA2StatisticsForPREDA,DataForPREDA-method Man page
DataForPREDA-class Man page
DataForPREDAMedianCenter Man page
DataForPREDAMedianCenter,DataForPREDA-method Man page
eset2GenomicAnnotations Man page
eset2GenomicAnnotations,ExpressionSet-method Man page
genomePlot Man page
genomePlot,GenomicAnnotationsForPREDA-method Man page
GenomicAnnotations2dataframe Man page
GenomicAnnotations2dataframe,GenomicAnnotationsForPREDA-method Man page
GenomicAnnotations2dataframe,GenomicAnnotations-method Man page
GenomicAnnotations2GenomicAnnotationsForPREDA Man page
GenomicAnnotations2GenomicAnnotationsForPREDA,GenomicAnnotations Man page
GenomicAnnotations2reference_positions Man page
GenomicAnnotations2reference_positions,GenomicAnnotations-method Man page
GenomicAnnotations-class Man page
GenomicAnnotationsExtract Man page
GenomicAnnotationsExtract,GenomicAnnotations-method Man page
GenomicAnnotationsFilter_neg Man page
GenomicAnnotationsFilter_neg,DataForPREDA-method Man page
GenomicAnnotationsFilter_neg,GenomicAnnotationsForPREDA-method Man page
GenomicAnnotationsFilter_neg,GenomicAnnotations-method Man page
GenomicAnnotationsFilter_pos Man page
GenomicAnnotationsFilter_pos,DataForPREDA-method Man page
GenomicAnnotationsFilter_pos,GenomicAnnotationsForPREDA-method Man page
GenomicAnnotationsFilter_pos,GenomicAnnotations-method Man page
GenomicAnnotationsForPREDA2dataframe Man page
GenomicAnnotationsForPREDA2dataframe,GenomicAnnotationsForPREDA- Man page
GenomicAnnotationsForPREDA2GenomicAnnotations Man page
GenomicAnnotationsForPREDA2GenomicAnnotations,GenomicAnnotations Man page
GenomicAnnotationsForPREDA2PREDAResults Man page
GenomicAnnotationsForPREDA2PREDAResults,GenomicAnnotationsForPRE Man page
GenomicAnnotationsForPREDA-class Man page
GenomicAnnotationsForPREDAFromfile Man page
GenomicAnnotationsFromdataframe Man page
GenomicAnnotationsFromfile Man page
GenomicAnnotationsFromLibrary Man page
GenomicAnnotationsSortAndCleanNA Man page
GenomicAnnotationsSortAndCleanNA,DataForPREDA-method Man page
GenomicAnnotationsSortAndCleanNA,GenomicAnnotationsForPREDA-meth Man page
GenomicAnnotationsSortAndCleanNA,GenomicAnnotations-method Man page
GenomicAnnotationsSortAndCleanNA,PREDADataAndResults-method Man page
GenomicAnnotationsSortAndCleanNA,PREDAResults-method Man page
GenomicRegions2dataframe Man page
GenomicRegionsAnnotate Man page
GenomicRegionsAnnotate,GenomicRegions,GenomicAnnotations-method Man page
GenomicRegionsChrNumber Man page
GenomicRegionsChrNumber,GenomicRegions-method Man page
GenomicRegions-class Man page
GenomicRegionsComparison Man page
GenomicRegionsComparison,GenomicRegions,GenomicRegions-method Man page
GenomicRegionsCreateRegionsIds Man page
GenomicRegionsCreateRegionsIds,GenomicRegions-method Man page
GenomicRegionsFilter_neg Man page
GenomicRegionsFilter_neg,GenomicRegions-method Man page
GenomicRegionsFilter_pos Man page
GenomicRegionsFilter_pos,GenomicRegions-method Man page
GenomicRegionsFindOverlap Man page
GenomicRegionsFromdataframe Man page
GenomicRegionsFromfile Man page
GenomicRegionsNumber Man page
GenomicRegionsNumber,GenomicRegions-method Man page
GenomicRegionsSpan Man page
GenomicRegionsSpan,GenomicRegions-method Man page
GenomicRegionsTotalSpan Man page
GenomicRegionsTotalSpan,GenomicRegions-method Man page
getStatisticByName Man page
getStatisticByName,StatisticsForPREDA-method Man page
MergeStatisticAnnotations2DataForPREDA Man page
PREDADataAndResults2dataframe Man page
PREDADataAndResults2dataframe,PREDADataAndResults-method Man page
PREDADataAndResults-class Man page
PREDA_main Man page
PREDAResults2dataframe Man page
PREDAResults2dataframe,PREDAResults-method Man page
PREDAResults2GenomicRegions Man page
PREDAResults2GenomicRegions,PREDAResults-method Man page
PREDAResults2GenomicRegionsSingle Man page
PREDAResults2GenomicRegionsSingle,PREDAResults-method Man page
PREDAResults2PREDADataAndResults Man page
PREDAResults2PREDADataAndResults,PREDAResults-method Man page
PREDAResults-class Man page
PREDAResultsGetObservedFlags Man page
PREDAResultsGetObservedFlags,PREDAResults-method Man page
preprocessingGE Man page
SODEGIR_GEstatistics Man page
SODEGIR_GEstatistics,ExpressionSet-method Man page
SODEGIRpreprocessingGE Man page
StatisticsForPREDA2dataframe Man page
StatisticsForPREDA2dataframe,StatisticsForPREDA-method Man page
StatisticsForPREDA-class Man page
StatisticsForPREDAFilterColumns_neg Man page
StatisticsForPREDAFilterColumns_neg,DataForPREDA-method Man page
StatisticsForPREDAFilterColumns_neg,StatisticsForPREDA-method Man page
StatisticsForPREDAFilterColumns_pos Man page
StatisticsForPREDAFilterColumns_pos,DataForPREDA-method Man page
StatisticsForPREDAFilterColumns_pos,StatisticsForPREDA-method Man page
StatisticsForPREDAFromdataframe Man page
statisticsForPREDAfromEset Man page
statisticsForPREDAfromEset,ExpressionSet-method Man page
StatisticsForPREDAFromfile Man page

Files

PREDA/.BBSoptions
PREDA/DESCRIPTION
PREDA/NAMESPACE
PREDA/R
PREDA/R/AllClasses.R PREDA/R/AllGenerics.R PREDA/R/CleanNAAnnotationDataframe.R PREDA/R/DataForPREDA2GenomicAnnotationsForPREDA.R PREDA/R/DataForPREDA2StatisticsForPREDA.R PREDA/R/DataForPREDA2dataframe.R PREDA/R/GE_computeStatistic.R PREDA/R/GEhighWeakExpressionWorkflow.R PREDA/R/GEsimulationsWorkflow.R PREDA/R/GenomicAnnotations2GenomicAnnotationsForPREDA.R PREDA/R/GenomicAnnotations2dataframe.R PREDA/R/GenomicAnnotations2reference_positions.R PREDA/R/GenomicAnnotationsExtract.R PREDA/R/GenomicAnnotationsFilter_neg.R PREDA/R/GenomicAnnotationsFilter_pos.R PREDA/R/GenomicAnnotationsForPREDA2GenomicAnnotations.R PREDA/R/GenomicAnnotationsForPREDA2PREDAResults.R PREDA/R/GenomicAnnotationsForPREDA2dataframe.R PREDA/R/GenomicAnnotationsForPREDAFromfile.R PREDA/R/GenomicAnnotationsForPREDAGetExpectedFlags.R PREDA/R/GenomicAnnotationsFromLibrary.R PREDA/R/GenomicAnnotationsFromdataframe.R PREDA/R/GenomicAnnotationsFromfile.R PREDA/R/GenomicAnnotationsSortAndCleanNA.R PREDA/R/GenomicRegions2dataframe.R PREDA/R/GenomicRegionsAnnotate.R PREDA/R/GenomicRegionsChrNumber.R PREDA/R/GenomicRegionsComparison.R PREDA/R/GenomicRegionsCreateRegionsIds.R PREDA/R/GenomicRegionsFilter_neg.R PREDA/R/GenomicRegionsFilter_pos.R PREDA/R/GenomicRegionsFindOverlap.R PREDA/R/GenomicRegionsFromdataframe.R PREDA/R/GenomicRegionsFromfile.R PREDA/R/GenomicRegionsNumber.R PREDA/R/GenomicRegionsSpan.R PREDA/R/GenomicRegionsTotalSpan.R PREDA/R/MergeStatisticAnnotations2DataForPREDA.R PREDA/R/PREDADataAndResults2dataframe.R PREDA/R/PREDAResults2GenomicRegions.R PREDA/R/PREDAResults2GenomicRegionsSingle.R PREDA/R/PREDAResults2PREDADataAndResults.R PREDA/R/PREDAResults2dataframe.R PREDA/R/PREDAResultsGetObservedFlags.R PREDA/R/PREDA_main.R PREDA/R/PREDA_main_permRows.R PREDA/R/PREDA_main_permSamples.R PREDA/R/PREDA_multTestCorrection.R PREDA/R/PREDA_quantsmoothStat.R PREDA/R/PREDA_quantsmoothStatPerm.R PREDA/R/PREDA_smoothStat.R PREDA/R/PREDA_smoothStatPerm.R PREDA/R/PREDA_splineStat.R PREDA/R/PREDA_splineStatPerm.R PREDA/R/RMAwithCDFfilter.R PREDA/R/SODEGIR_GEstatistics.R PREDA/R/SODEGIRpreprocessingGE.R PREDA/R/SortAnnotationDataframe.R PREDA/R/StatisticsForPREDA2dataframe.R PREDA/R/StatisticsForPREDAFilterColumns_neg.R PREDA/R/StatisticsForPREDAFilterColumns_pos.R PREDA/R/StatisticsForPREDAFromdataframe.R PREDA/R/StatisticsForPREDAFromfile.R PREDA/R/analysesNames.R PREDA/R/compareFunctionFromStatisticsForPREDA.R PREDA/R/computeDatasetSignature.R PREDA/R/datasetSignatureFromFlags.R PREDA/R/eset2GenomicAnnotations.R PREDA/R/genomePlot.R PREDA/R/genomePlot_improved.R PREDA/R/getExpectedSmoothFunction.R PREDA/R/getExpectedSmoothFunction_runmean.R PREDA/R/getObservedSmoothFunction.R PREDA/R/getObservedSmoothFunction_runmean.R PREDA/R/getStatisticByName.R PREDA/R/initialize-methods.R PREDA/R/preprocessingGE.R PREDA/R/simulations.R PREDA/R/statisticsForPREDAfromEset.R
PREDA/build
PREDA/build/vignette.rds
PREDA/inst
PREDA/inst/doc
PREDA/inst/doc/PREDAclasses.Rnw
PREDA/inst/doc/PREDAclasses.pdf
PREDA/inst/doc/PREDAtutorial.R
PREDA/inst/doc/PREDAtutorial.Rnw
PREDA/inst/doc/PREDAtutorial.pdf
PREDA/man
PREDA/man/DataForPREDA-class.Rd PREDA/man/DataForPREDA2GenomicAnnotationsForPREDA.Rd PREDA/man/DataForPREDA2StatisticsForPREDA.Rd PREDA/man/DataForPREDA2dataframe.Rd PREDA/man/DataForPREDAMedianCenter.Rd PREDA/man/GenomicAnnotations-class.Rd PREDA/man/GenomicAnnotations2GenomicAnnotationsForPREDA.Rd PREDA/man/GenomicAnnotations2dataframe.Rd PREDA/man/GenomicAnnotations2reference_positions.Rd PREDA/man/GenomicAnnotationsExtract.Rd PREDA/man/GenomicAnnotationsFilter_neg.Rd PREDA/man/GenomicAnnotationsFilter_pos.Rd PREDA/man/GenomicAnnotationsForPREDA-class.Rd PREDA/man/GenomicAnnotationsForPREDA2GenomicAnnotations.Rd PREDA/man/GenomicAnnotationsForPREDA2PREDAResults.Rd PREDA/man/GenomicAnnotationsForPREDA2dataframe.Rd PREDA/man/GenomicAnnotationsForPREDAFromfile.Rd PREDA/man/GenomicAnnotationsFromLibrary.Rd PREDA/man/GenomicAnnotationsFromdataframe.Rd PREDA/man/GenomicAnnotationsFromfile.Rd PREDA/man/GenomicAnnotationsSortAndCleanNA.Rd PREDA/man/GenomicRegions-class.Rd PREDA/man/GenomicRegions2dataframe.Rd PREDA/man/GenomicRegionsAnnotate.Rd PREDA/man/GenomicRegionsChrNumber.Rd PREDA/man/GenomicRegionsComparison.Rd PREDA/man/GenomicRegionsCreateRegionsIds.Rd PREDA/man/GenomicRegionsFilter_neg.Rd PREDA/man/GenomicRegionsFilter_pos.Rd PREDA/man/GenomicRegionsFindOverlap.Rd PREDA/man/GenomicRegionsFromdataframe.Rd PREDA/man/GenomicRegionsFromfile.Rd PREDA/man/GenomicRegionsNumber.Rd PREDA/man/GenomicRegionsSpan.Rd PREDA/man/GenomicRegionsTotalSpan.Rd PREDA/man/MergeStatisticAnnotations2DataForPREDA.Rd PREDA/man/PREDADataAndResults-class.Rd PREDA/man/PREDADataAndResults2dataframe.Rd PREDA/man/PREDAResults-class.Rd PREDA/man/PREDAResults2GenomicRegions.Rd PREDA/man/PREDAResults2GenomicRegionsSingle.Rd PREDA/man/PREDAResults2PREDADataAndResults.Rd PREDA/man/PREDAResults2dataframe.Rd PREDA/man/PREDAResultsGetObservedFlags.Rd PREDA/man/PREDA_main.Rd PREDA/man/SODEGIR_GEstatistics.Rd PREDA/man/SODEGIRpreprocessingGE.Rd PREDA/man/StatisticsForPREDA-class.Rd PREDA/man/StatisticsForPREDA2dataframe.Rd PREDA/man/StatisticsForPREDAFilterColumns_neg.Rd PREDA/man/StatisticsForPREDAFilterColumns_pos.Rd PREDA/man/StatisticsForPREDAFromdataframe.Rd PREDA/man/StatisticsForPREDAFromfile.Rd PREDA/man/analysesNames.Rd PREDA/man/computeDatasetSignature.Rd PREDA/man/eset2GenomicAnnotations.Rd PREDA/man/genomePlot.Rd PREDA/man/getStatisticByName.Rd PREDA/man/preprocessingGE.Rd PREDA/man/statisticsForPREDAfromEset.Rd
PREDA/vignettes
PREDA/vignettes/PREDA.bib
PREDA/vignettes/PREDAclasses.Rnw
PREDA/vignettes/PREDAtutorial.Rnw
PREDA/vignettes/PREDAtutorial.bbl
PREDA/vignettes/images
PREDA/vignettes/images/PREDA_inputClasses.png
PREDA/vignettes/images/PREDA_inputoutputClasses.png
PREDA/vignettes/images/PREDA_outputClasses.png
PREDA/vignettes/images/sodegirWorkflow.png

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