ESEA

Package: ESEA
Version: 1.0
Title: ESEA: Discovering the Dysregulated Pathways based on Edge Set
Enrichment Analysis
Author: Junwei Han, Xinrui Shi, Chunquan Li
Maintainer: Xinrui Shi <xinrui103@163.com>
Description: 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.
Depends: R (>= 2.10), igraph, XML, parmigene
Suggests: Matrix, graph
Collate: calEdgeCorScore.R ESEA.Main.R PlotGlobEdgeCorProfile.R
PlotPathwayGraph.R PlotRunEnrichment.R SavePathway2File.R
getEnvironmentData.R GetExampleData.R GetEdgesBackgrandData.R
GetPathwayEdgeData.R
LazyData: Yes
License: GPL (>= 2)
biocViews: Statistics, Pathways, edge, enrichment analysis
Packaged: 2015-01-22 12:50:32 UTC; Administrator
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-22 15:58:44

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ESEA' ...
** package 'ESEA' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ESEA'
    finding HTML links ... done
    ESEA-internal                           html  
    ESEA.Main                               html  
    EdgesBackgrandData                      html  
    ExampleData                             html  
    GetEdgesBackgrandData                   html  
    GetExampleData                          html  
    GetPathwayEdgeData                      html  
    PathwayEdgeData                         html  
    PlotGlobEdgeCorProfile                  html  
    PlotPathwayGraph                        html  
    finding level-2 HTML links ... done

    PlotRunEnrichment                       html  
    SavePathway2File                        html  
    calEdgeCorScore                         html  
    envData                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ESEA)
Making 'packages.html' ... done