OmicsExampleData        Omics example dataset.
PWidentallprots         Identification of pathwayIDs and pathway names
                        for all proteins.
PWidentallprotssub      Internal subfunction for all protein pathway
                        identification.
PWidenttps              Identification of pathwayIDs and pathway names
                        for proteins at individual timepoints.
SteinerTree_cons        Steiner tree algorithm.
TFidentallgenes         Identification of upstream transcription
                        factors for all genes.
TFidenttps              Identification of upstream transcription
                        factors.
addFeedbackLoops        Add feedback loops from target genes to
                        proteins/TFs if present.
clusterTimeProfiles     Clustering of time profiles.
consDynamicNet          Dynamic analysis.
createBiopaxnew         Create a new Biopax model containing all
                        database information.
createIntIDs            Create internal IDs.
findSignalingAxes       Find downstream signaling axis.
findxneighborsoverlap   Find overlap of next neighbors of transcription
                        factors in identified pathways.
findxnextneighbors      Find next neighbors of transcription factors in
                        identified pathways. Produces a list of x next
                        neighbors for each transcription factor in the
                        pathway.
genGenelists            Generate genelists from pathway databases.
genGenelistssub         Generate internally genelists from pathway
                        databases.
genIntIDs               Internal function for generation of pathway
                        database specific internal IDs.
generate_DSSignalingBase
                        Generate a folder with downstream information
                        about all phosphoproteins.
genfullConsensusGraph   Combine SteinerNet with bipartite graph to get
                        full consensus network.
getAlias_Ensemble       Get Gene Symbols from Ensemble Gene Accession
                        IDs.
getAliasfromSTRINGIDs   Map alias names to STRING IDs of consensus
                        graph.
getBiopaxModel          Get upstream regulators of identified
                        transcription factors.
getConsensusSTRINGIDs   Get consensus graph in STRING IDs.
getDS_PWs               Get downstream analysis pathways.
getDS_TFs               Get downstream analysis transcription factors
                        in pathways.
getDS_TGs               Get downstream analysis target genes of TFs
                        found in pathways.
getFCsplines            Get fold change splines.
getGenesIntersection    Get genes intersection for the omics data on
                        the different time points.
getOmicsDataset         Get Omics dataset.
getOmicsTimepoints      Get Omics timepoints.
getOmicsallGeneIDs      Get all gene IDs.
getOmicsallProteinIDs   Get all protein IDs.
getProteinIntersection
                        Get protein intersection for the omics data on
                        the different time points. The timepoints or
                        measurement names for comparison have to be
                        defined in tp_prot and tp_genes as given in the
                        readOmics function.
getSTRING_graph         Generate STRING PPI graph.
getTFIntersection       Get TF intersection for the omics data on the
                        different time points.
getUS_PWs               Get upstream pathways of identified
                        transcription factors.
getUS_TFs               Get upstream TFs.
getUS_regulators        Get upstream regulators of identified
                        transcription factors.
get_matching_transcripts
                        Summarize table of matching downstream
                        transcripts.
getbipartitegraphInfo   Get TF-target gene information for the
                        consensus graph.
gettpIntersection       Get omics data intersection on the three
                        levels. Get intersection for the omics data on
                        all three levels (proteins, TFs, genes) on
                        corresponding time points.
identPWsofTFs           Identification of pathways containing the
                        transcription factors identified in upstream
                        analysis
identRegulators         Identify overlapping upstream regulators of x
                        transcription factors
identTFTGsinPWs         Prepare OmicsData object for pathway
                        information.
identTFs                This function provides a data.table of upstream
                        transcription factors.
identifyPR              Identify phosphorylation regulation influence
                        downstream
identifyPWTFTGs         Identify TFs in pathways and their target genes
                        - downstream analysis.
identifyPWs             Identify pathway IDs and pathway names of
                        differentially abundant proteins
identifyRsofTFs         Identify regulators of transcription factors -
                        upstream analysis.
identifyTFs             Transcription factor identification.
infoConsensusGraph      Add Consensus Graph information.
loadGenelists           Loading of genelists
loadPWs                 Load pathway database information.
plotConsDynNet          Plot inferred net based on analysis analysis.
plotConsensusGraph      Plot consensus graph(s) from static analysis.
plotConsensusProfiles   Plot consensus graph profiles of static
                        consensus molecules.
plotTimeProfileClusters
                        Plot time profile clusters of dynamic analysis
                        result.
predictFCvals           Prediction of continous data points via
                        smoothing splines.
preparePWinfo           Prepare OmicsData object for pathway
                        information.
print.OmicsData         Print an OmicsData object.
pwIntOmics-package      Pathway-based data integration of omics data
readOmics               Read in omics data.
readPWdata              Read in pathway database data needed for
                        pathway identification.
readPhosphodata         Reads in phosphoprotein downstream regulation
                        information.
readTFdata              Reads in chosen transcription factor target
                        database information.
readTFtargets           Read in matching transcription factor target
                        gene pairs.
selectPWsofTFs          Select pathways with more than x TFs
staticConsensusNet      Static analysis.
temp_correlations       Plot temporal correlations of phosphoprotein
                        expression levels and affected downstream
                        transcripts.
