Man pages for pwOmics
Pathway-based data integration of omics data

addFeedbackLoopsAdd feedback loops from target genes to proteins/TFs if...
clusterTimeProfilesClustering of time profiles.
consDynamicNetDynamic analysis.
createBiopaxnewCreate a new Biopax model containing all database...
createIntIDsCreate internal IDs.
findSignalingAxesFind downstream signaling axis.
findxneighborsoverlapFind overlap of next neighbors of transcription factors in...
findxnextneighborsFind next neighbors of transcription factors in identified...
generate_DSSignalingBaseGenerate a folder with downstream information about all...
genfullConsensusGraphCombine SteinerNet with bipartite graph to get full consensus...
genGenelistsGenerate genelists from pathway databases.
genGenelistssubGenerate internally genelists from pathway databases.
genIntIDsInternal function for generation of pathway database specific...
getAlias_EnsembleGet Gene Symbols from Ensemble Gene Accession IDs.
getAliasfromSTRINGIDsMap alias names to STRING IDs of consensus graph.
getBiopaxModelGet upstream regulators of identified transcription factors.
getbipartitegraphInfoGet TF-target gene information for the consensus graph.
getConsensusSTRINGIDsGet consensus graph in STRING IDs.
getDS_PWsGet downstream analysis pathways.
getDS_TFsGet downstream analysis transcription factors in pathways.
getDS_TGsGet downstream analysis target genes of TFs found in...
getFCsplinesGet fold change splines.
getGenesIntersectionGet genes intersection for the omics data on the different...
get_matching_transcriptsSummarize table of matching downstream transcripts.
getOmicsallGeneIDsGet all gene IDs.
getOmicsallProteinIDsGet all protein IDs.
getOmicsDatasetGet Omics dataset.
getOmicsTimepointsGet Omics timepoints.
getProteinIntersectionGet protein intersection for the omics data on the different...
getSTRING_graphGenerate STRING PPI graph.
getTFIntersectionGet TF intersection for the omics data on the different time...
gettpIntersectionGet omics data intersection on the three levels. Get...
getUS_PWsGet upstream pathways of identified transcription factors.
getUS_regulatorsGet upstream regulators of identified transcription factors.
getUS_TFsGet upstream TFs.
identifyPRIdentify phosphorylation regulation influence downstream
identifyPWsIdentify pathway IDs and pathway names of differentially...
identifyPWTFTGsIdentify TFs in pathways and their target genes - downstream...
identifyRsofTFsIdentify regulators of transcription factors - upstream...
identifyTFsTranscription factor identification.
identPWsofTFsIdentification of pathways containing the transcription...
identRegulatorsIdentify overlapping upstream regulators of x transcription...
identTFsThis function provides a data.table of upstream transcription...
identTFTGsinPWsPrepare OmicsData object for pathway information.
loadGenelistsLoading of genelists
loadPWsLoad pathway database information.
OmicsExampleDataOmics example dataset.
plotConsDynNetPlot inferred net based on analysis analysis.
plotConsensusGraphPlot consensus graph(s) from static analysis.
plotConsensusProfilesPlot consensus graph profiles of static consensus molecules.
plotTimeProfileClustersPlot time profile clusters of dynamic analysis result.
predictFCvalsPrediction of continous data points via smoothing splines.
preparePWinfoPrepare OmicsData object for pathway information.
print.OmicsDataPrint an OmicsData object.
PWidentallprotsIdentification of pathwayIDs and pathway names for all...
PWidentallprotssubInternal subfunction for all protein pathway identification.
PWidenttpsIdentification of pathwayIDs and pathway names for proteins...
pwIntOmics-packagePathway-based data integration of omics data
readOmicsRead in omics data.
readPhosphodataReads in phosphoprotein downstream regulation information.
readPWdataRead in pathway database data needed for pathway...
readTFdataReads in chosen transcription factor target database...
readTFtargetsRead in matching transcription factor target gene pairs.
selectPWsofTFsSelect pathways with more than x TFs
staticConsensusNetStatic analysis.
SteinerTree_consSteiner tree algorithm.
temp_correlationsPlot temporal correlations of phosphoprotein expression...
TFidentallgenesIdentification of upstream transcription factors for all...
TFidenttpsIdentification of upstream transcription factors.
pwOmics documentation built on May 31, 2017, 11:11 a.m.