Package: PREDA 1.51.0

Francesco Ferrari

PREDA: Position Related Data Analysis

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

Authors:Francesco Ferrari <[email protected]>

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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-1.51.0(bioc 3.20)PREDA-1.50.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

53 exports 1.85 score 48 dependencies 5 mentions

Last updated 2 months agofrom:6a76d46d67

Dependencies:annotate AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite KEGGREST lattice lifecycle lokern MASS Matrix memoise mime multtest openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors sfsmisc survival sys UCSC.utils vctrs XML xtable XVector zlibbioc

PREDA S4-classes

Rendered fromPREDAclasses.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2018-09-14
Started: 2013-11-01

PREDA tutorial

Rendered fromPREDAtutorial.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2018-09-14
Started: 2013-11-01

Citation

Development and contributors

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