# Pathway-based data integration of omics data

## Documentation for package ‘pwOmics’ version 1.30.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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.