ESEA: ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

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The package can identify the dysregulated canonical pathways by investigating the changes of biological relationships of pathways in the context of gene expression data. (1) The ESEA package constructs a background set of edges by extracting pathway structure (e.g. interaction, regulation, modification, and binding etc.) from the seven public databases (KEGG; Reactome; Biocarta; NCI; SPIKE; HumanCyc; Panther) and the edge sets of pathways for each of the above databases. (2) The ESEA package can can quantify the change of correlation between genes for each edge based on gene expression data with cases and controls. (3) The ESEA package uses the weighted Kolmogorov-Smirnov statistic to calculate an edge enrichment score (EES), which reflects the degree to which a given pathway is associated the specific phenotype. (4) The ESEA package can provide the visualization of the results.

Author
Junwei Han, Xinrui Shi, Chunquan Li
Date of publication
2015-01-22 15:58:44
Maintainer
Xinrui Shi <xinrui103@163.com>
License
GPL (>= 2)
Version
1.0

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Man pages

calEdgeCorScore
Calculate the differential correlation score for edges
EdgesBackgrandData
The data for the background set of edges
envData
The variables in the environment variable 'envData' of the...
ESEA-internal
ESEA internal functions
ESEA.Main
Identify dysregulated pathways based on edge set enrichment...
ExampleData
The example data in the environment variable of the system
GetEdgesBackgrandData
Get the data for background set of edges
GetExampleData
Get the example data
GetPathwayEdgeData
Get the edge sets of pathways
PathwayEdgeData
The edge sets of pathways
PlotGlobEdgeCorProfile
Plot global edge correlation profile
PlotPathwayGraph
Plot the pathway-result network diagram
PlotRunEnrichment
Plot running Edge enrichment score
SavePathway2File
Save a pathway-result network to a file which can be input to...

Files in this package

ESEA
ESEA/inst
ESEA/inst/doc
ESEA/inst/doc/ESEA.R
ESEA/inst/doc/ESEA.pdf
ESEA/inst/doc/ESEA.Rnw
ESEA/NAMESPACE
ESEA/data
ESEA/data/envData.rda
ESEA/data/datalist
ESEA/R
ESEA/R/PlotPathwayGraph.R
ESEA/R/GetPathwayEdgeData.R
ESEA/R/PlotGlobEdgeCorProfile.R
ESEA/R/calEdgeCorScore.R
ESEA/R/GetExampleData.R
ESEA/R/PlotRunEnrichment.R
ESEA/R/GetEdgesBackgrandData.R
ESEA/R/ESEA.Main.R
ESEA/R/SavePathway2File.R
ESEA/R/getEnvironmentData.R
ESEA/vignettes
ESEA/vignettes/ESEA.Rnw
ESEA/MD5
ESEA/build
ESEA/build/vignette.rds
ESEA/DESCRIPTION
ESEA/man
ESEA/man/PlotGlobEdgeCorProfile.Rd
ESEA/man/calEdgeCorScore.Rd
ESEA/man/GetPathwayEdgeData.Rd
ESEA/man/PlotPathwayGraph.Rd
ESEA/man/PathwayEdgeData.Rd
ESEA/man/ExampleData.Rd
ESEA/man/ESEA.Main.Rd
ESEA/man/EdgesBackgrandData.Rd
ESEA/man/SavePathway2File.Rd
ESEA/man/envData.Rd
ESEA/man/ESEA-internal.Rd
ESEA/man/GetEdgesBackgrandData.Rd
ESEA/man/PlotRunEnrichment.Rd
ESEA/man/GetExampleData.Rd