SubpathwayGMir

Package: SubpathwayGMir
Type: Package
Title: Identify Metabolic Subpathways Mediated by MicroRNAs
Version: 1.0
Date: 2015-05-20
Author: Li Feng, Chunquan Li and Xia Li
Maintainer: Li Feng <biofengfeng@sina.com>
Description: Routines for identifying metabolic subpathways mediated by microRNAs (miRNAs) through topologically locating miRNAs and genes within reconstructed Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway graphs embedded by miRNAs. (1) This package can obtain the reconstructed KEGG metabolic pathway graphs with genes and miRNAs as nodes, through converting KEGG metabolic pathways to graphs with genes as nodes and compounds as edges, and then integrating miRNA-target interactions verified by low-throughput experiments from four databases (TarBase, miRecords, mirTarBase and miR2Disease) into converted pathway graphs. (2) This package can locate metabolic subpathways mediated by miRNAs by topologically analyzing the "lenient distance" of miRNAs and genes within reconstructed KEGG metabolic pathway graphs.(3) This package can identify significantly enriched miRNA-mediated metabolic subpathways based on located subpathways by hypergenomic test. (4) This package can support six species for metabolic subpathway identification, such as caenorhabditis elegans, drosophila melanogaster, danio rerio, homo sapiens, mus musculus and rattus norvegicus, and user only need to update interested organism-specific environment variables.
Depends: R (>= 3.0.2), XML, igraph
Collate: fdr.est.R getBackground.R getEdgeLabel.R getEdgeLty.R
getInteGraphList.R GetK2riData.R getLayout.R getLocSubGraph.R
getOneNodePath.R getSymbolFromGene.R identifyGraph.R
initializeK2ri.R plotGraph.R printGraph.R updateOrgEnvir.R
mytriangle.R
LazyData: Yes
License: GPL (>= 2)
biocViews: Statistics, Annotation, SubPathways, Graphs, MicroRNAs
Packaged: 2015-05-20 06:50:06 UTC; sunyao
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-20 14:15:38

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SubpathwayGMir' ...
** package 'SubpathwayGMir' 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 'SubpathwayGMir'
    finding HTML links ... done
    GetK2riData                             html  
    SubpathwayGMir-internal                 html  
    SubpathwayGMir-package                  html  
    getBackground                           html  
    getInteGraphList                        html  
    getLocSubGraph                          html  
    finding level-2 HTML links ... done

    identifyGraph                           html  
    initializeK2ri                          html  
    plotGraph                               html  
    printGraph                              html  
    updateOrgEnvir                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SubpathwayGMir)
Making 'packages.html' ... done