pwOmics v1.4.0

by Astrid Wachter

Pathway-based data integration of omics data

pwOmics performs pathway-based level-specific data comparison of matching omics data sets based on pre-analysed user-specified lists of differential genes/transcripts and proteins. A separate downstream analysis of proteomic data including pathway identification and enrichment analysis, transcription factor identification and target gene identification is opposed to the upstream analysis starting with gene or transcript information as basis for identification of upstream transcription factors and regulators. The cross-platform comparative analysis allows for comprehensive analysis of single time point experiments and time-series experiments by providing static and dynamic analysis tools for data integration.

Functions in pwOmics

Name Description
TFidentallgenes Identification of upstream transcription factors for all genes.
findxneighborsoverlap Find overlap of next neighbors of transcription factors in identified pathways.
getGenesIntersection Get genes intersection for the omics data on the different time points.
getAliasfromSTRINGIDs Map alias names to STRING IDs of consensus graph.
genGenelists Generate genelists from pathway databases.
getOmicsallGeneIDs Get all gene IDs.
genGenelistssub Generate internally genelists from pathway databases.
TFidenttps Identification of upstream transcription factors.
getTFIntersection Get TF intersection for the omics data on the different time points.
SteinerTree_cons Steiner tree algorithm.
identTFTGsinPWs Prepare OmicsData object for pathway information.
getBiopaxModel Get upstream regulators of identified transcription factors.
getUS_regulators Get upstream regulators of identified transcription factors.
getUS_TFs Get upstream TFs.
PWidenttps Identification of pathwayIDs and pathway names for proteins at individual timepoints.
getUS_PWs Get upstream pathways of identified transcription factors.
enrichTFs Transcription factor enrichment - upstream analysis.
getOmicsallProteinIDs Get all protein IDs.
plotConsensusProfiles Plot consensus graph profiles of static consensus molecules.
findxnextneighbors Find next neighbors of transcription factors in identified pathways.
PWidentallprotssub Internal subfunction for all protein pathway identification.
getProteinIntersection Get protein intersection for the omics data on the different time points.
identifyPWs Identify pathway IDs and pathway names of differentially abundant proteins
preparePWinfo Prepare OmicsData object for pathway information.
getConsensusSTRINGIDs Get consensus graph in STRING IDs.
addFeedbackLoops Add feedback loops from target genes to proteins/TFs if present.
getDS_TGs Get downstream analysis target genes of TFs found in pathways.
readOmics Read in omics data.
gettpIntersection Get omics data intersection on the three levels.
identPWsofTFs Identification of pathways containing the transcription factors identified in upstream analysis
getbipartitegraphInfo Get TF-target gene information for the consensus graph.
getAlias_Ensemble Get Gene Symbols from Ensemble Gene Accession IDs.
getSTRING_graph Generate STRING PPI graph.
plotTimeProfileClusters Plot time profile clusters of dynamic analysis result.
identifyTFs Transcription factor identification.
plotConsDynNet Plot inferred net based on analysis analysis.
readTFtargets Read in matching transcription factor target gene pairs.
identifyPWTFTGs Identify TFs in enriched pathways and their target genes - downstream analysis.
readTFdata Reads in chosen transcription factor target database information.
clusterTimeProfiles Clustering of time profiles.
genfullConsensusGraph Combine SteinerNet with bipartite graph to get full consensus network.
getOmicsDataset Get Omics dataset.
getOmicsTimepoints Get Omics timepoints.
readPWdata Read in pathway database data needed for pathway identification.
staticConsensusNet Static analysis.
getDS_TFs Get downstream analysis transcription factors in pathways.
print.OmicsData Print an OmicsData object.
createIntIDs Create internal IDs.
getFCsplines Get fold change splines.
plotConsensusGraph Plot consensus graph(s) from static analysis.
identifyRsofTFs Identify regulators of enriched transcription factors - upstream analysis.
pwIntOmics-package Pathway-based data integration of omics data
selectPWsofTFs Select pathways with more than x TFs
loadGenelists Loading of genelists
createBiopaxnew Create a new Biopax model containing all database information.
consDynamicNet Dynamic analysis.
genIntIDs Internal function for generation of pathway database specific internal IDs.
PWidentallprots Identification of pathwayIDs and pathway names for all proteins.
OmicsExampleData Omics example dataset.
enrichPWs Pathway enrichment - downstream analysis.
getDS_PWs Get downstream analysis pathways.
identTFs This function provides a data.table of upstream transcription factors and the flag for enrichment.
loadPWs Load pathway database information.
predictFCvals Prediction of continous data points via smoothing splines.
identRegulators Identify overlapping upstream regulators of x transcription factors
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Details

Type Package
Date 2014-12-29
License GPL (>= 2)
biocViews SystemsBiology, Transcription, GeneTarget
NeedsCompilation no
imports AnnotationDbi , AnnotationHub , Biobase , BiocGenerics , biomaRt , data , data.table , GenomicRanges , gplots , graphics , igraph , rBiopaxParser , STRINGdb
depends base (>= 3.2) , R (>= 3.2)
suggests ebdbNet , longitudinal , Mfuzz
Contributors Astrid Wachter

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