Package: PREDA 1.53.0
Francesco Ferrari
PREDA: Position Related Data Analysis
Package for the position related analysis of quantitative functional genomics data.
Authors:
PREDA_1.53.0.tar.gz
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PREDA.pdf |PREDA.html✨
PREDA/json (API)
| # Install 'PREDA' in R: |
| install.packages('PREDA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:PREDA-1.53.0(bioc 3.21)PREDA-1.52.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarecopynumbervariationgeneexpressiongenetics
Last updated 2 months agofrom:431f3f6087. Checks:OK: 1 WARNING: 3 ERROR: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | ERROR | Dec 19 2024 |
| R-4.5-linux | WARNING | Dec 19 2024 |
| R-4.4-win | ERROR | Dec 19 2024 |
| R-4.4-mac | WARNING | Dec 19 2024 |
| R-4.3-win | ERROR | Dec 19 2024 |
| R-4.3-mac | WARNING | Dec 19 2024 |
Exports:analysesNamescomputeDatasetSignatureDataForPREDA2dataframeDataForPREDA2GenomicAnnotationsForPREDADataForPREDA2StatisticsForPREDADataForPREDAMedianCentereset2GenomicAnnotationsgenomePlotGenomicAnnotations2dataframeGenomicAnnotations2GenomicAnnotationsForPREDAGenomicAnnotations2reference_positionsGenomicAnnotationsExtractGenomicAnnotationsFilter_negGenomicAnnotationsFilter_posGenomicAnnotationsForPREDA2dataframeGenomicAnnotationsForPREDA2GenomicAnnotationsGenomicAnnotationsForPREDA2PREDAResultsGenomicAnnotationsForPREDAFromfileGenomicAnnotationsFromdataframeGenomicAnnotationsFromfileGenomicAnnotationsFromLibraryGenomicAnnotationsSortAndCleanNAGenomicRegions2dataframeGenomicRegionsAnnotateGenomicRegionsChrNumberGenomicRegionsComparisonGenomicRegionsCreateRegionsIdsGenomicRegionsFilter_negGenomicRegionsFilter_posGenomicRegionsFindOverlapGenomicRegionsFromdataframeGenomicRegionsFromfileGenomicRegionsNumberGenomicRegionsSpanGenomicRegionsTotalSpangetStatisticByNameMergeStatisticAnnotations2DataForPREDAPREDA_mainPREDADataAndResults2dataframePREDAResults2dataframePREDAResults2GenomicRegionsPREDAResults2GenomicRegionsSinglePREDAResults2PREDADataAndResultsPREDAResultsGetObservedFlagspreprocessingGESODEGIR_GEstatisticsSODEGIRpreprocessingGEStatisticsForPREDA2dataframeStatisticsForPREDAFilterColumns_negStatisticsForPREDAFilterColumns_posStatisticsForPREDAFromdataframestatisticsForPREDAfromEsetStatisticsForPREDAFromfile
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlatticelifecyclelokernMASSMatrixmemoisemimemulttestopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorssfsmiscsurvivalsysUCSC.utilsvctrsXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get the names of the analyses in the from PREDA objects | analysesNames analysesNames,PREDAResults-method analysesNames,StatisticsForPREDA-method |
| Function to compute dataset signature for recurrent significant genomic regions | computeDatasetSignature computeDatasetSignature,GenomicAnnotationsForPREDA-method |
| Class "DataForPREDA" is used to manage all of the data required as input for PREDA analysis | DataForPREDA-class |
| extract data and annotations as a dataframe | DataForPREDA2dataframe DataForPREDA2dataframe,DataForPREDA-method |
| extract a GenomicAnnotationsForPREDA object from a data DataForPREDA object | DataForPREDA2GenomicAnnotationsForPREDA DataForPREDA2GenomicAnnotationsForPREDA,DataForPREDA-method |
| extract a StatisticsForPREDA object from a data DataForPREDA object | DataForPREDA2StatisticsForPREDA DataForPREDA2StatisticsForPREDA,DataForPREDA-method |
| Function to scale median value of DataForPREDA statistics to zero | DataForPREDAMedianCenter DataForPREDAMedianCenter,DataForPREDA-method |
| Function building a GenomicAnnotations object on an ExpressionSet object | eset2GenomicAnnotations eset2GenomicAnnotations,ExpressionSet-method |
| draw a genome plot | genomePlot genomePlot,GenomicAnnotationsForPREDA-method |
| Class "GenomicAnnotations" to manage information about genomic features | GenomicAnnotations-class |
| extracts annotations as a dataframe | GenomicAnnotations2dataframe GenomicAnnotations2dataframe,GenomicAnnotations-method GenomicAnnotations2dataframe,GenomicAnnotationsForPREDA-method |
| generate a GenomicAnnotationsForPREDA object from a GenomicAnnotations object | GenomicAnnotations2GenomicAnnotationsForPREDA GenomicAnnotations2GenomicAnnotationsForPREDA,GenomicAnnotations-method |
| extract reference positions from the GenomicAnnotations | GenomicAnnotations2reference_positions GenomicAnnotations2reference_positions,GenomicAnnotations-method |
| extract optional annotations for a specific region | GenomicAnnotationsExtract GenomicAnnotationsExtract,GenomicAnnotations-method |
| filter annotations to remove selected chromosomes | GenomicAnnotationsFilter_neg GenomicAnnotationsFilter_neg,DataForPREDA-method GenomicAnnotationsFilter_neg,GenomicAnnotations-method GenomicAnnotationsFilter_neg,GenomicAnnotationsForPREDA-method |
| filter annotations to keep selected chromosomes | GenomicAnnotationsFilter_pos GenomicAnnotationsFilter_pos,DataForPREDA-method GenomicAnnotationsFilter_pos,GenomicAnnotations-method GenomicAnnotationsFilter_pos,GenomicAnnotationsForPREDA-method |
| Class "GenomicAnnotationsForPREDA" GenomicAnnotations class with additional slot specifying the reference position for PREDA analysis | GenomicAnnotationsForPREDA-class |
| extract annotations as a dataframe | GenomicAnnotationsForPREDA2dataframe GenomicAnnotationsForPREDA2dataframe,GenomicAnnotationsForPREDA-method |
| extract the GenomicAnnotations object from the GenomicAnnotationsForPREDA object | GenomicAnnotationsForPREDA2GenomicAnnotations GenomicAnnotationsForPREDA2GenomicAnnotations,GenomicAnnotationsForPREDA-method |
| add PREDA results information to genomic annotatations creating a PREDAResults object | GenomicAnnotationsForPREDA2PREDAResults GenomicAnnotationsForPREDA2PREDAResults,GenomicAnnotationsForPREDA-method |
| Function to create a GenomicAnnotationsForPREDA object from a txt file | GenomicAnnotationsForPREDAFromfile |
| Function to create a GenomiAnnotations object from a dataframe | GenomicAnnotationsFromdataframe |
| Function to create a GenomiAnnotations object from a text file | GenomicAnnotationsFromfile |
| Function extracting a GenomicAnnotations object from a Bioconductor annotation library | GenomicAnnotationsFromLibrary |
| sort annotations according to selected chromosomes and to remove genes containing any NA annotation field | GenomicAnnotationsSortAndCleanNA GenomicAnnotationsSortAndCleanNA,DataForPREDA-method GenomicAnnotationsSortAndCleanNA,GenomicAnnotations-method GenomicAnnotationsSortAndCleanNA,GenomicAnnotationsForPREDA-method GenomicAnnotationsSortAndCleanNA,PREDADataAndResults-method GenomicAnnotationsSortAndCleanNA,PREDAResults-method |
| Class "GenomicRegions" is used to manage information about genomic regions | GenomicRegions-class |
| extract genomic regions information as a dataframe object | GenomicRegions2dataframe |
| extract annotations from a GenomicAnnotations object for a set of regions specified as a GenomicRegions object | GenomicRegionsAnnotate GenomicRegionsAnnotate,GenomicRegions,GenomicAnnotations-method |
| determine the number of chromosomes with genomic regions | GenomicRegionsChrNumber GenomicRegionsChrNumber,GenomicRegions-method |
| compare GenomicRegions objects to identify overlaps and differences | GenomicRegionsComparison GenomicRegionsComparison,GenomicRegions,GenomicRegions-method |
| generate unique ids for GenomicRegions objects | GenomicRegionsCreateRegionsIds GenomicRegionsCreateRegionsIds,GenomicRegions-method |
| filter genomic regions to remove selected chromosomes | GenomicRegionsFilter_neg GenomicRegionsFilter_neg,GenomicRegions-method |
| filter genomic regions to keep selected chromosomes | GenomicRegionsFilter_pos GenomicRegionsFilter_pos,GenomicRegions-method |
| Function to find overlap between GenomicRegions objects | GenomicRegionsFindOverlap |
| Function to create a GenomiRegions object from a dataframe | GenomicRegionsFromdataframe |
| Function to create a GenomiRegions object from a text file | GenomicRegionsFromfile |
| determine the number of genomic regions | GenomicRegionsNumber GenomicRegionsNumber,GenomicRegions-method |
| determine the span of each genomic region | GenomicRegionsSpan GenomicRegionsSpan,GenomicRegions-method |
| determine the total span of genomic regions | GenomicRegionsTotalSpan GenomicRegionsTotalSpan,GenomicRegions-method |
| extract data for individual analyses using the analysis name | getStatisticByName getStatisticByName,StatisticsForPREDA-method |
| Merge a StatisticsForPREDA and a GenomicAnnotationsForPREDA object into a DataForPREDA object. | MergeStatisticAnnotations2DataForPREDA |
| function performing the core of PREDA analysis | PREDA_main |
| Class "PREDADataAndResults" is used to manage the PREDA analysis output | PREDADataAndResults-class |
| extract data and annotations as a dataframe with probeids as rownames | PREDADataAndResults2dataframe PREDADataAndResults2dataframe,PREDADataAndResults-method |
| Class "PREDAResults" ~is used to manage the PREDA analysis output | PREDAResults-class |
| extact preda results statistics as a data frame object | PREDAResults2dataframe PREDAResults2dataframe,PREDAResults-method |
| identify significant genomic regions from a PREDAResults object | PREDAResults2GenomicRegions PREDAResults2GenomicRegions,PREDAResults-method |
| identify significant genomic regions from a single analysis in a PREDAResults object | PREDAResults2GenomicRegionsSingle PREDAResults2GenomicRegionsSingle,PREDAResults-method |
| merge PREDAResults and input statistics to create a PREDADataAndResults object | PREDAResults2PREDADataAndResults PREDAResults2PREDADataAndResults,PREDAResults-method |
| extract genomic positions with significant alterations as a matrix of flags from a PREDAResults object | PREDAResultsGetObservedFlags PREDAResultsGetObservedFlags,PREDAResults-method |
| Wrapper function for gene expression data preprocessing for differential expression analysis with PREDA | preprocessingGE |
| Wrapper function for gene expression statistics preprocessing for SODEGIR analysis | SODEGIR_GEstatistics SODEGIR_GEstatistics,ExpressionSet-method |
| Wrapper function for gene expression data preprocessing for SODEGIR analysis | SODEGIRpreprocessingGE |
| Class "StatisticsForPREDA" is used to manage the datamatrix containing statistics for PREDA analyses | StatisticsForPREDA-class |
| extract data as a dataframe with probeids as rownames | StatisticsForPREDA2dataframe StatisticsForPREDA2dataframe,StatisticsForPREDA-method |
| filter statistics to remove selected analyses | StatisticsForPREDAFilterColumns_neg StatisticsForPREDAFilterColumns_neg,DataForPREDA-method StatisticsForPREDAFilterColumns_neg,StatisticsForPREDA-method |
| filter statistics to keep selected analyses | StatisticsForPREDAFilterColumns_pos StatisticsForPREDAFilterColumns_pos,DataForPREDA-method StatisticsForPREDAFilterColumns_pos,StatisticsForPREDA-method |
| Function to create a StatisticsForPREDA objet from a dataframe | StatisticsForPREDAFromdataframe |
| function to compute a statisticsForPREDA object from an ExpressionSet object | statisticsForPREDAfromEset statisticsForPREDAfromEset,ExpressionSet-method |
| Function to create a StatisticsForPREDA objet from a txt file | StatisticsForPREDAFromfile |
