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. |
enrichPWs | Pathway enrichment - downstream analysis. |
enrichTFs | Transcription factor enrichment - upstream analysis. |
findxneighborsoverlap | Find overlap of next neighbors of transcription factors in identified pathways. |
findxnextneighbors | Find next neighbors of transcription factors in identified pathways. |
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. |
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. |
getUS_PWs | Get upstream pathways of identified transcription factors. |
getUS_regulators | Get upstream regulators of identified transcription factors. |
getUS_TFs | Get upstream TFs. |
identifyPWs | Identify pathway IDs and pathway names of differentially abundant proteins |
identifyPWTFTGs | Identify TFs in enriched pathways and their target genes - downstream analysis. |
identifyRsofTFs | Identify regulators of enriched 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 and the flag for enrichment. |
identTFTGsinPWs | Prepare OmicsData object for pathway 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. |
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. |
TFidentallgenes | Identification of upstream transcription factors for all genes. |
TFidenttps | Identification of upstream transcription factors. |