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pwOmics (version 1.4.0)

Pathway-based data integration of omics data

Description

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.

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Version

Version

1.4.0

License

GPL (>= 2)

Maintainer

Astrid Wachter

Last Published

February 15th, 2017

Functions in pwOmics (1.4.0)

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