Pathway-based data integration of omics data

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Documentation for package ‘pwOmics’ version 1.30.0

• DESCRIPTION file.
• Package NEWS.

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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.