Man pages for Bioconductor-mirror/PREDA
Position Related Data Analysis

analysesNamesGet the names of the analyses in the from PREDA objects
computeDatasetSignatureFunction to compute dataset signature for recurrent...
DataForPREDA2dataframeextract data and annotations as a dataframe
DataForPREDA2GenomicAnnotationsForPREDAextract a GenomicAnnotationsForPREDA object from a data...
DataForPREDA2StatisticsForPREDAextract a StatisticsForPREDA object from a data DataForPREDA...
DataForPREDA-classClass "DataForPREDA" is used to manage all of the data...
DataForPREDAMedianCenterFunction to scale median value of DataForPREDA statistics to...
eset2GenomicAnnotationsFunction building a GenomicAnnotations object on an...
genomePlotdraw a genome plot
GenomicAnnotations2dataframeextracts annotations as a dataframe
GenomicAnnotations2GenomicAnnotationsForPREDAgenerate a GenomicAnnotationsForPREDA object from a...
GenomicAnnotations2reference_positionsextract reference positions from the GenomicAnnotations
GenomicAnnotations-classClass "GenomicAnnotations" to manage information about...
GenomicAnnotationsExtractextract optional annotations for a specific region
GenomicAnnotationsFilter_negfilter annotations to remove selected chromosomes
GenomicAnnotationsFilter_posfilter annotations to keep selected chromosomes
GenomicAnnotationsForPREDA2dataframeextract annotations as a dataframe
GenomicAnnotationsForPREDA2GenomicAnnotationsextract the GenomicAnnotations object from the...
GenomicAnnotationsForPREDA2PREDAResultsadd PREDA results information to genomic annotatations...
GenomicAnnotationsForPREDA-classClass "GenomicAnnotationsForPREDA" GenomicAnnotations class...
GenomicAnnotationsForPREDAFromfileFunction to create a GenomicAnnotationsForPREDA object from a...
GenomicAnnotationsFromdataframeFunction to create a GenomiAnnotations object from a...
GenomicAnnotationsFromfileFunction to create a GenomiAnnotations object from a text...
GenomicAnnotationsFromLibraryFunction extracting a GenomicAnnotations object from a...
GenomicAnnotationsSortAndCleanNAsort annotations according to selected chromosomes and to...
GenomicRegions2dataframeextract genomic regions information as a dataframe object
GenomicRegionsAnnotateextract annotations from a GenomicAnnotations object for a...
GenomicRegionsChrNumberdetermine the number of chromosomes with genomic regions
GenomicRegions-classClass "GenomicRegions" is used to manage information about...
GenomicRegionsComparisoncompare GenomicRegions objects to identify overlaps and...
GenomicRegionsCreateRegionsIdsgenerate unique ids for GenomicRegions objects
GenomicRegionsFilter_negfilter genomic regions to remove selected chromosomes
GenomicRegionsFilter_posfilter genomic regions to keep selected chromosomes
GenomicRegionsFindOverlapFunction to find overlap between GenomicRegions objects
GenomicRegionsFromdataframeFunction to create a GenomiRegions object from a dataframe
GenomicRegionsFromfileFunction to create a GenomiRegions object from a text file
GenomicRegionsNumberdetermine the number of genomic regions
GenomicRegionsSpandetermine the span of each genomic region
GenomicRegionsTotalSpandetermine the total span of genomic regions
getStatisticByNameextract data for individual analyses using the analysis name
MergeStatisticAnnotations2DataForPREDAMerge a StatisticsForPREDA and a GenomicAnnotationsForPREDA...
PREDADataAndResults2dataframeextract data and annotations as a dataframe with probeids as...
PREDADataAndResults-classClass "PREDADataAndResults" is used to manage the PREDA...
PREDA_mainfunction performing the core of PREDA analysis
PREDAResults2dataframeextact preda results statistics as a data frame object
PREDAResults2GenomicRegionsidentify significant genomic regions from a PREDAResults...
PREDAResults2GenomicRegionsSingleidentify significant genomic regions from a single analysis...
PREDAResults2PREDADataAndResultsmerge PREDAResults and input statistics to create a...
PREDAResults-classClass "PREDAResults" ~is used to manage the PREDA analysis...
PREDAResultsGetObservedFlagsextract genomic positions with significant alterations as a...
preprocessingGEWrapper function for gene expression data preprocessing for...
SODEGIR_GEstatisticsWrapper function for gene expression statistics preprocessing...
SODEGIRpreprocessingGEWrapper function for gene expression data preprocessing for...
StatisticsForPREDA2dataframeextract data as a dataframe with probeids as rownames
StatisticsForPREDA-classClass "StatisticsForPREDA" is used to manage the datamatrix...
StatisticsForPREDAFilterColumns_negfilter statistics to remove selected analyses
StatisticsForPREDAFilterColumns_posfilter statistics to keep selected analyses
StatisticsForPREDAFromdataframeFunction to create a StatisticsForPREDA objet from a...
statisticsForPREDAfromEsetfunction to compute a statisticsForPREDA object from an...
StatisticsForPREDAFromfileFunction to create a StatisticsForPREDA objet from a txt file
Bioconductor-mirror/PREDA documentation built on May 31, 2017, 9:41 p.m.