PREDA: Position Related Data Analysis
Version 1.22.0

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

AuthorFrancesco Ferrari <francesco.ferrari@ifom.eu>
Bioconductor views CopyNumberVariation GeneExpression Genetics Software
Date of publicationNone
MaintainerFrancesco Ferrari <francesco.ferrari@ifom.eu>
LicenseGPL-2
Version1.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PREDA")

Popular man pages

GenomicAnnotations2dataframe: extracts annotations as a dataframe
GenomicAnnotationsForPREDA2GenomicAnnotations: extract the GenomicAnnotations object from the...
GenomicAnnotationsFromdataframe: Function to create a GenomiAnnotations object from a...
GenomicAnnotationsSortAndCleanNA: sort annotations according to selected chromosomes and to...
GenomicRegions-class: Class "GenomicRegions" is used to manage information about...
GenomicRegionsTotalSpan: determine the total span of genomic regions
statisticsForPREDAfromEset: function to compute a statisticsForPREDA object from an...
See all...

All man pages Function index File listing

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

CleanNAAnnotationDataframe Source code
DataForPREDA-class Man page
DataForPREDA2GenomicAnnotationsForPREDA Man page
DataForPREDA2GenomicAnnotationsForPREDA,DataForPREDA-method Man page
DataForPREDA2StatisticsForPREDA Man page
DataForPREDA2StatisticsForPREDA,DataForPREDA-method Man page
DataForPREDA2dataframe Man page
DataForPREDA2dataframe,DataForPREDA-method Man page
DataForPREDAMedianCenter Man page
DataForPREDAMedianCenter,DataForPREDA-method Man page
EvaluateSimulationPerformance Source code
GE_computeStatistic_onMatrix Source code
GE_sample_rows Source code
GE_simulations_samplingColumns_onMatrix Source code
GenomicAnnotations-class Man page
GenomicAnnotations2GenomicAnnotationsForPREDA Man page
GenomicAnnotations2GenomicAnnotationsForPREDA,GenomicAnnotations Man page
GenomicAnnotations2dataframe Man page
GenomicAnnotations2dataframe,GenomicAnnotations-method Man page
GenomicAnnotations2dataframe,GenomicAnnotationsForPREDA-method Man page
GenomicAnnotations2reference_positions Man page
GenomicAnnotations2reference_positions,GenomicAnnotations-method Man page
GenomicAnnotationsExtract Man page
GenomicAnnotationsExtract,GenomicAnnotations-method Man page
GenomicAnnotationsFilter_neg Man page
GenomicAnnotationsFilter_neg,DataForPREDA-method Man page
GenomicAnnotationsFilter_neg,GenomicAnnotations-method Man page
GenomicAnnotationsFilter_neg,GenomicAnnotationsForPREDA-method Man page
GenomicAnnotationsFilter_pos Man page
GenomicAnnotationsFilter_pos,DataForPREDA-method Man page
GenomicAnnotationsFilter_pos,GenomicAnnotations-method Man page
GenomicAnnotationsFilter_pos,GenomicAnnotationsForPREDA-method Man page
GenomicAnnotationsForPREDA-class Man page
GenomicAnnotationsForPREDA2GenomicAnnotations Man page
GenomicAnnotationsForPREDA2GenomicAnnotations,GenomicAnnotations Man page
GenomicAnnotationsForPREDA2PREDAResults Man page
GenomicAnnotationsForPREDA2PREDAResults,GenomicAnnotationsForPRE Man page
GenomicAnnotationsForPREDA2dataframe Man page
GenomicAnnotationsForPREDA2dataframe,GenomicAnnotationsForPREDA- Man page
GenomicAnnotationsForPREDAFromfile Man page Source code
GenomicAnnotationsFromLibrary Man page Source code
GenomicAnnotationsFromdataframe Man page Source code
GenomicAnnotationsFromfile Man page Source code
GenomicAnnotationsSortAndCleanNA Man page
GenomicAnnotationsSortAndCleanNA,DataForPREDA-method Man page
GenomicAnnotationsSortAndCleanNA,GenomicAnnotations-method Man page
GenomicAnnotationsSortAndCleanNA,GenomicAnnotationsForPREDA-meth Man page
GenomicAnnotationsSortAndCleanNA,PREDADataAndResults-method Man page
GenomicAnnotationsSortAndCleanNA,PREDAResults-method Man page
GenomicRegions-class Man page
GenomicRegions2dataframe Man page Source code
GenomicRegionsAnnotate Man page
GenomicRegionsAnnotate,GenomicRegions,GenomicAnnotations-method Man page
GenomicRegionsChrNumber Man page
GenomicRegionsChrNumber,GenomicRegions-method 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 Source code
GenomicRegionsFromdataframe Man page Source code
GenomicRegionsFromfile Man page Source code
GenomicRegionsNumber Man page
GenomicRegionsNumber,GenomicRegions-method Man page
GenomicRegionsSpan Man page
GenomicRegionsSpan,GenomicRegions-method Man page
GenomicRegionsTotalSpan Man page
GenomicRegionsTotalSpan,GenomicRegions-method Man page
MergeStatisticAnnotations2DataForPREDA Man page Source code
PREDADataAndResults-class Man page
PREDADataAndResults2dataframe Man page
PREDADataAndResults2dataframe,PREDADataAndResults-method Man page
PREDAResults-class 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
PREDAResults2dataframe Man page
PREDAResults2dataframe,PREDAResults-method Man page
PREDAResultsGetObservedFlags Man page
PREDAResultsGetObservedFlags,PREDAResults-method Man page
PREDA_main Man page Source code
PREDA_main_permRows Source code
PREDA_main_permSamples Source code
PREDA_multTestCorrection Source code
PREDA_quantsmoothStat Source code
PREDA_quantsmoothStatPerm Source code
PREDA_smoothStat Source code
PREDA_smoothStatPerm Source code
PREDA_splineStat Source code
PREDA_splineStatPerm Source code
RMAwithCDFfilter Source code
SODEGIR_GEstatistics Man page
SODEGIR_GEstatistics,ExpressionSet-method Man page
SODEGIRpreprocessingGE Man page Source code
SortAnnotationDataframe Source code
StatisticsForPREDA-class Man page
StatisticsForPREDA2dataframe Man page
StatisticsForPREDA2dataframe,StatisticsForPREDA-method 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 Source code
StatisticsForPREDAFromfile Man page Source code
analysesNames Man page
analysesNames,PREDAResults-method Man page
analysesNames,StatisticsForPREDA-method Man page
computeDatasetSignature Man page
computeDatasetSignature,GenomicAnnotationsForPREDA-method Man page
datasetSignatureFromFlags Source code
datasetSignatureFromFlags_getFrequencies Source code
eset2GenomicAnnotations Man page
eset2GenomicAnnotations,ExpressionSet-method Man page
genomePlot Man page
genomePlot,GenomicAnnotationsForPREDA-method Man page
genomePlot_improved Source code
getExpectedSmoothFunction Source code
getExpectedSmoothFunction_runmean Source code
getObservedSmoothFunction Source code
getObservedSmoothFunction_runmean Source code
getPermutationMatrix Source code
getStardadizeFunction Source code
getStatisticByName Man page
getStatisticByName,StatisticsForPREDA-method Man page
preprocessingGE Man page Source code
statisticsForPREDAfromEset Man page
statisticsForPREDAfromEset,ExpressionSet-method Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/CleanNAAnnotationDataframe.R
R/DataForPREDA2GenomicAnnotationsForPREDA.R
R/DataForPREDA2StatisticsForPREDA.R
R/DataForPREDA2dataframe.R
R/GE_computeStatistic.R
R/GEhighWeakExpressionWorkflow.R
R/GEsimulationsWorkflow.R
R/GenomicAnnotations2GenomicAnnotationsForPREDA.R
R/GenomicAnnotations2dataframe.R
R/GenomicAnnotations2reference_positions.R
R/GenomicAnnotationsExtract.R
R/GenomicAnnotationsFilter_neg.R
R/GenomicAnnotationsFilter_pos.R
R/GenomicAnnotationsForPREDA2GenomicAnnotations.R
R/GenomicAnnotationsForPREDA2PREDAResults.R
R/GenomicAnnotationsForPREDA2dataframe.R
R/GenomicAnnotationsForPREDAFromfile.R
R/GenomicAnnotationsForPREDAGetExpectedFlags.R
R/GenomicAnnotationsFromLibrary.R
R/GenomicAnnotationsFromdataframe.R
R/GenomicAnnotationsFromfile.R
R/GenomicAnnotationsSortAndCleanNA.R
R/GenomicRegions2dataframe.R
R/GenomicRegionsAnnotate.R
R/GenomicRegionsChrNumber.R
R/GenomicRegionsComparison.R
R/GenomicRegionsCreateRegionsIds.R
R/GenomicRegionsFilter_neg.R
R/GenomicRegionsFilter_pos.R
R/GenomicRegionsFindOverlap.R
R/GenomicRegionsFromdataframe.R
R/GenomicRegionsFromfile.R
R/GenomicRegionsNumber.R
R/GenomicRegionsSpan.R
R/GenomicRegionsTotalSpan.R
R/MergeStatisticAnnotations2DataForPREDA.R
R/PREDADataAndResults2dataframe.R
R/PREDAResults2GenomicRegions.R
R/PREDAResults2GenomicRegionsSingle.R
R/PREDAResults2PREDADataAndResults.R
R/PREDAResults2dataframe.R
R/PREDAResultsGetObservedFlags.R
R/PREDA_main.R
R/PREDA_main_permRows.R
R/PREDA_main_permSamples.R
R/PREDA_multTestCorrection.R
R/PREDA_quantsmoothStat.R
R/PREDA_quantsmoothStatPerm.R
R/PREDA_smoothStat.R
R/PREDA_smoothStatPerm.R
R/PREDA_splineStat.R
R/PREDA_splineStatPerm.R
R/RMAwithCDFfilter.R
R/SODEGIR_GEstatistics.R
R/SODEGIRpreprocessingGE.R
R/SortAnnotationDataframe.R
R/StatisticsForPREDA2dataframe.R
R/StatisticsForPREDAFilterColumns_neg.R
R/StatisticsForPREDAFilterColumns_pos.R
R/StatisticsForPREDAFromdataframe.R
R/StatisticsForPREDAFromfile.R
R/analysesNames.R
R/compareFunctionFromStatisticsForPREDA.R
R/computeDatasetSignature.R
R/datasetSignatureFromFlags.R
R/eset2GenomicAnnotations.R
R/genomePlot.R
R/genomePlot_improved.R
R/getExpectedSmoothFunction.R
R/getExpectedSmoothFunction_runmean.R
R/getObservedSmoothFunction.R
R/getObservedSmoothFunction_runmean.R
R/getStatisticByName.R
R/initialize-methods.R
R/preprocessingGE.R
R/simulations.R
R/statisticsForPREDAfromEset.R
build
build/vignette.rds
inst
inst/doc
inst/doc/PREDAclasses.Rnw
inst/doc/PREDAclasses.pdf
inst/doc/PREDAtutorial.R
inst/doc/PREDAtutorial.Rnw
inst/doc/PREDAtutorial.pdf
man
man/DataForPREDA-class.Rd
man/DataForPREDA2GenomicAnnotationsForPREDA.Rd
man/DataForPREDA2StatisticsForPREDA.Rd
man/DataForPREDA2dataframe.Rd
man/DataForPREDAMedianCenter.Rd
man/GenomicAnnotations-class.Rd
man/GenomicAnnotations2GenomicAnnotationsForPREDA.Rd
man/GenomicAnnotations2dataframe.Rd
man/GenomicAnnotations2reference_positions.Rd
man/GenomicAnnotationsExtract.Rd
man/GenomicAnnotationsFilter_neg.Rd
man/GenomicAnnotationsFilter_pos.Rd
man/GenomicAnnotationsForPREDA-class.Rd
man/GenomicAnnotationsForPREDA2GenomicAnnotations.Rd
man/GenomicAnnotationsForPREDA2PREDAResults.Rd
man/GenomicAnnotationsForPREDA2dataframe.Rd
man/GenomicAnnotationsForPREDAFromfile.Rd
man/GenomicAnnotationsFromLibrary.Rd
man/GenomicAnnotationsFromdataframe.Rd
man/GenomicAnnotationsFromfile.Rd
man/GenomicAnnotationsSortAndCleanNA.Rd
man/GenomicRegions-class.Rd
man/GenomicRegions2dataframe.Rd
man/GenomicRegionsAnnotate.Rd
man/GenomicRegionsChrNumber.Rd
man/GenomicRegionsComparison.Rd
man/GenomicRegionsCreateRegionsIds.Rd
man/GenomicRegionsFilter_neg.Rd
man/GenomicRegionsFilter_pos.Rd
man/GenomicRegionsFindOverlap.Rd
man/GenomicRegionsFromdataframe.Rd
man/GenomicRegionsFromfile.Rd
man/GenomicRegionsNumber.Rd
man/GenomicRegionsSpan.Rd
man/GenomicRegionsTotalSpan.Rd
man/MergeStatisticAnnotations2DataForPREDA.Rd
man/PREDADataAndResults-class.Rd
man/PREDADataAndResults2dataframe.Rd
man/PREDAResults-class.Rd
man/PREDAResults2GenomicRegions.Rd
man/PREDAResults2GenomicRegionsSingle.Rd
man/PREDAResults2PREDADataAndResults.Rd
man/PREDAResults2dataframe.Rd
man/PREDAResultsGetObservedFlags.Rd
man/PREDA_main.Rd
man/SODEGIR_GEstatistics.Rd
man/SODEGIRpreprocessingGE.Rd
man/StatisticsForPREDA-class.Rd
man/StatisticsForPREDA2dataframe.Rd
man/StatisticsForPREDAFilterColumns_neg.Rd
man/StatisticsForPREDAFilterColumns_pos.Rd
man/StatisticsForPREDAFromdataframe.Rd
man/StatisticsForPREDAFromfile.Rd
man/analysesNames.Rd
man/computeDatasetSignature.Rd
man/eset2GenomicAnnotations.Rd
man/genomePlot.Rd
man/getStatisticByName.Rd
man/preprocessingGE.Rd
man/statisticsForPREDAfromEset.Rd
vignettes
vignettes/PREDA.bib
vignettes/PREDAclasses.Rnw
vignettes/PREDAtutorial.Rnw
vignettes/images
vignettes/images/PREDA_inputClasses.png
vignettes/images/PREDA_inputoutputClasses.png
vignettes/images/PREDA_outputClasses.png
vignettes/images/sodegirWorkflow.png
PREDA documentation built on May 20, 2017, 10:55 p.m.

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