PREDA: Position RElated Data Anlysis

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

Author
Francesco Ferrari <francesco.ferrari@unimore.it>
Date of publication
None
Maintainer
Francesco Ferrari <francesco.ferrari@unimore.it>
License
GPL-2
Version
1.20.0

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

Files in this package

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