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PREDA (version 1.18.0)

Position RElated Data Anlysis

Description

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

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Version

Version

1.18.0

License

GPL-2

Maintainer

Francesco Ferrari

Last Published

February 15th, 2017

Functions in PREDA (1.18.0)

GenomicAnnotations-class

Class "GenomicAnnotations" to manage information about genomic features
GenomicAnnotationsFilter_pos

filter annotations to keep selected chromosomes
GenomicRegionsChrNumber

determine the number of chromosomes with genomic regions
GenomicRegionsCreateRegionsIds

generate unique ids for GenomicRegions objects
GenomicAnnotationsForPREDA-class

Class "GenomicAnnotationsForPREDA" GenomicAnnotations class with additional slot specifying the reference position for PREDA analysis
StatisticsForPREDAFromdataframe

Function to create a StatisticsForPREDA objet from a dataframe
GenomicAnnotationsForPREDA2dataframe

extract annotations as a dataframe
DataForPREDAMedianCenter

Function to scale median value of DataForPREDA statistics to zero
GenomicRegionsAnnotate

extract annotations from a GenomicAnnotations object for a set of regions specified as a GenomicRegions object
getStatisticByName

extract data for individual analyses using the analysis name
MergeStatisticAnnotations2DataForPREDA

Merge a StatisticsForPREDA and a GenomicAnnotationsForPREDA object into a DataForPREDA object.
PREDADataAndResults-class

Class "PREDADataAndResults" is used to manage the PREDA analysis output
genomePlot

draw a genome plot
PREDA_main

function performing the core of PREDA analysis
PREDAResults2dataframe

extact preda results statistics as a data frame object
GenomicAnnotations2GenomicAnnotationsForPREDA

generate a GenomicAnnotationsForPREDA object from a GenomicAnnotations object
GenomicAnnotations2dataframe

extracts annotations as a dataframe
GenomicAnnotationsFromfile

Function to create a GenomiAnnotations object from a text file
DataForPREDA2StatisticsForPREDA

extract a StatisticsForPREDA object from a data DataForPREDA object
GenomicAnnotationsFromLibrary

Function extracting a GenomicAnnotations object from a Bioconductor annotation library
GenomicAnnotationsForPREDA2GenomicAnnotations

extract the GenomicAnnotations object from the GenomicAnnotationsForPREDA object
GenomicRegionsComparison

compare GenomicRegions objects to identify overlaps and differences
GenomicAnnotations2reference_positions

extract reference positions from the GenomicAnnotations
computeDatasetSignature

Function to compute dataset signature for recurrent significant genomic regions
eset2GenomicAnnotations

Function building a GenomicAnnotations object on an ExpressionSet object
GenomicAnnotationsSortAndCleanNA

sort annotations according to selected chromosomes and to remove genes containing any NA annotation field
preprocessingGE

Wrapper function for gene expression data preprocessing for differential expression analysis with PREDA
PREDAResults2GenomicRegions

identify significant genomic regions from a PREDAResults object
GenomicRegionsFindOverlap

Function to find overlap between GenomicRegions objects
statisticsForPREDAfromEset

function to compute a statisticsForPREDA object from an ExpressionSet object
PREDAResults-class

Class "PREDAResults" ~is used to manage the PREDA analysis output
StatisticsForPREDAFilterColumns_neg

filter statistics to remove selected analyses
analysesNames

Get the names of the analyses in the from PREDA objects
DataForPREDA2GenomicAnnotationsForPREDA

extract a GenomicAnnotationsForPREDA object from a data DataForPREDA object
GenomicRegionsFromfile

Function to create a GenomiRegions object from a text file
PREDAResultsGetObservedFlags

extract genomic positions with significant alterations as a matrix of flags from a PREDAResults object
PREDAResults2GenomicRegionsSingle

identify significant genomic regions from a single analysis in a PREDAResults object
StatisticsForPREDA-class

Class "StatisticsForPREDA" is used to manage the datamatrix containing statistics for PREDA analyses
SODEGIRpreprocessingGE

Wrapper function for gene expression data preprocessing for SODEGIR analysis
SODEGIR_GEstatistics

Wrapper function for gene expression statistics preprocessing for SODEGIR analysis
DataForPREDA-class

Class "DataForPREDA" is used to manage all of the data required as input for PREDA analysis
GenomicAnnotationsExtract

extract optional annotations for a specific region
GenomicAnnotationsFromdataframe

Function to create a GenomiAnnotations object from a dataframe
GenomicAnnotationsFilter_neg

filter annotations to remove selected chromosomes
PREDAResults2PREDADataAndResults

merge PREDAResults and input statistics to create a PREDADataAndResults object
GenomicAnnotationsForPREDAFromfile

Function to create a GenomicAnnotationsForPREDA object from a txt file
StatisticsForPREDAFromfile

Function to create a StatisticsForPREDA objet from a txt file
StatisticsForPREDAFilterColumns_pos

filter statistics to keep selected analyses
GenomicRegionsTotalSpan

determine the total span of genomic regions
DataForPREDA2dataframe

extract data and annotations as a dataframe
GenomicRegions-class

Class "GenomicRegions" is used to manage information about genomic regions
GenomicRegionsNumber

determine the number of genomic regions
GenomicRegionsFromdataframe

Function to create a GenomiRegions object from a dataframe
GenomicAnnotationsForPREDA2PREDAResults

add PREDA results information to genomic annotatations creating a PREDAResults object
GenomicRegions2dataframe

extract genomic regions information as a dataframe object
GenomicRegionsFilter_pos

filter genomic regions to keep selected chromosomes
GenomicRegionsSpan

determine the span of each genomic region
GenomicRegionsFilter_neg

filter genomic regions to remove selected chromosomes
PREDADataAndResults2dataframe

extract data and annotations as a dataframe with probeids as rownames
StatisticsForPREDA2dataframe

extract data as a dataframe with probeids as rownames