Pathway-based data integration of omics data

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Documentation for package ‘pwOmics’ version 1.14.0

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pwIntOmics-package Pathway-based data integration of omics data
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.
generate_DSSignalingBase Generate a folder with downstream information about all phosphoproteins.
genfullConsensusGraph Combine SteinerNet with bipartite graph to get full consensus network.
genGenelists Generate genelists from pathway databases.
genGenelistssub Generate internally genelists from pathway databases.
genIntIDs Internal function for generation of pathway database specific internal IDs.
getAliasfromSTRINGIDs Map alias names to STRING IDs of consensus graph.
getAlias_Ensemble Get Gene Symbols from Ensemble Gene Accession IDs.
getBiopaxModel Get upstream regulators of identified transcription factors.
getbipartitegraphInfo Get TF-target gene information for the consensus graph.
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.
getOmicsallGeneIDs Get all gene IDs.
getOmicsallProteinIDs Get all protein IDs.
getOmicsDataset Get Omics dataset.
getOmicsTimepoints Get Omics timepoints.
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.
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.
getUS_PWs Get upstream pathways of identified transcription factors.
getUS_regulators Get upstream regulators of identified transcription factors.
getUS_TFs Get upstream TFs.
get_matching_transcripts Summarize table of matching downstream transcripts.
identifyPR Identify phosphorylation regulation influence downstream
identifyPWs Identify pathway IDs and pathway names of differentially abundant proteins
identifyPWTFTGs Identify TFs in pathways and their target genes - downstream analysis.
identifyRsofTFs Identify regulators of transcription factors - upstream analysis.
identifyTFs Transcription factor identification.
identPWsofTFs Identification of pathways containing the transcription factors identified in upstream analysis
identRegulators Identify overlapping upstream regulators of x transcription factors
identTFs This function provides a data.table of upstream transcription factors.
identTFTGsinPWs Prepare OmicsData object for pathway information.
infoConsensusGraph Add Consensus Graph information.
loadGenelists Loading of genelists
loadPWs Load pathway database information.
OmicsExampleData Omics example dataset.
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.
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.
pwIntOmics Pathway-based data integration of omics data
readOmics Read in omics data.
readPhosphodata Reads in phosphoprotein downstream regulation information.
readPWdata Read in pathway database data needed for pathway identification.
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.
SteinerTree_cons Steiner tree algorithm.
temp_correlations Plot temporal correlations of phosphoprotein expression levels and affected downstream transcripts.
TFidentallgenes Identification of upstream transcription factors for all genes.
TFidenttps Identification of upstream transcription factors.