Man pages for MarenS2/pwOmics_maren
Pathway-based data integration of omics data
| addFeedbackLoops | Add feedback loops from target genes to proteins/TFs if... |
| clusterTimeProfiles | Clustering of time profiles. |
| consDynamicNet | Dynamic analysis. |
| createBiopaxnew | Create a new Biopax model containing all database... |
| createIntIDs | Create internal IDs. |
| findSignalingAxes | Find downstream signaling axis. |
| findxneighborsoverlap | Find overlap of next neighbors of transcription factors in... |
| findxnextneighbors | Find next neighbors of transcription factors in identified... |
| generate_DSSignalingBase | Generate a folder with downstream information about all... |
| genfullConsensusGraph | Combine SteinerNet with bipartite graph to get full consensus... |
| genGenelists | Generate genelists from pathway databases. |
| genGenelistssub | Generate internally genelists from pathway databases. |
| genIntIDs | Internal function for generation of pathway database specific... |
| 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. |
| 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... |
| getFCsplines | Get fold change splines. |
| getGenesIntersection | Get genes intersection for the omics data on the different... |
| get_matching_transcripts | Summarize table of matching downstream transcripts. |
| 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... |
| getSTRING_graph | Generate STRING PPI graph. |
| getTFIntersection | Get TF intersection for the omics data on the different time... |
| gettpIntersection | Get omics data intersection on the three levels. Get... |
| getUS_PWs | Get upstream pathways of identified transcription factors. |
| getUS_regulators | Get upstream regulators of identified transcription factors. |
| getUS_TFs | Get upstream TFs. |
| identifyPR | Identify phosphorylation regulation influence downstream |
| identifyPWs | Identify pathway IDs and pathway names of differentially... |
| identifyPWTFTGs | Identify TFs in pathways and their target genes - downstream... |
| identifyRsofTFs | Identify regulators of transcription factors - upstream... |
| identifyTFs | Transcription factor identification. |
| identPWsofTFs | Identification of pathways containing the transcription... |
| identRegulators | Identify overlapping upstream regulators of x transcription... |
| identTFs | This function provides a data.table of upstream transcription... |
| 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... |
| PWidentallprotssub | Internal subfunction for all protein pathway identification. |
| PWidenttps | Identification of pathwayIDs and pathway names for proteins... |
| pwIntOmics-package | 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... |
| readTFdata | Reads in chosen transcription factor target database... |
| 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... |
| TFidentallgenes | Identification of upstream transcription factors for all... |
| TFidenttps | Identification of upstream transcription factors. |
