PROFANCY: The package can prioritize candidate disease metabolites based on global functional relationships between metabolites in the context of metabolic pathways
Version 1.0

The package can prioritize the candidate disease metabolites based on the assumption that functionally related metabolites tend to associate with the same or similar diseases in the context of metabolic pathway. The PROFANCY package (1) prioritizes the disease metabolites from global functional similarity and local modularity of the metabolic network; (2) allows users to select default metabolites or input their interested metabolites as seed nodes or candidate nodes (3) can prioritize the candidate metabolites in KEGG or EHMN metabolic network.

AuthorQianlan Yao, Desi Shang, Chunquan Li
Bioconductor views Disease Metabolites Network RandomWalk;
Date of publication2013-07-12 08:58:53
MaintainerQianlan Yao <yaoqianlan@yahoo.com>
LicenseGPL (>= 2)
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PROFANCY")

Popular man pages

aaa-PROFANCY-package: The PROFANCY package
envData: The variables in the environment variable envData of the...
getCandidates: Get candidate metabolites
getProvidedDiseaseName: Get all disease names provided by PROFANCY package
getSeed: Get seed metabolites
getTopDiseaseMetabolites: Get the disease Risk metabolites
initializeData: initialize environment envData
See all...

All man pages Function index File listing

Man pages

aaa-PROFANCY-package: The PROFANCY package
envData: The variables in the environment variable envData of the...
getCandidates: Get candidate metabolites
getProvidedDiseaseName: Get all disease names provided by PROFANCY package
getSeed: Get seed metabolites
getTopDiseaseMetabolites: Get the disease Risk metabolites
initializeData: initialize environment envData
PROFANCY-internal: PROFANCY internal functions

Functions

DiseaseInfList Man page
EHMNAddPathInfNetwork Man page
KEGGAddPathInfNetwork Man page
MetaboliteInf Man page
PROFANCY Man page
PROFANCY-package Man page
ProstateCandidates Man page
ProstateSeeds Man page
RandomWalk2igraph Man page Source code
envData Man page
getCandidates Man page Source code
getGraph Man page Source code
getPriList Man page Source code
getProvidedDiseaseName Man page Source code
getSeed Man page Source code
getTopDiseaseMetabolites Man page Source code
initializeData Man page Source code
rw Man page Source code

Files

MD5
NAMESPACE
vignettes
vignettes/PROFANCY.Rnw
R
R/getTopDiseaseMetaboliteList.R
man
man/PROFANCY-internal.Rd
man/initializeData.Rd
man/getTopDiseaseMetabolites.Rd
man/getSeed.Rd
man/getProvidedDiseaseName.Rd
man/getCandidates.Rd
man/envData.Rd
man/aaa-PROFANCY-package.Rd
inst
inst/doc
inst/doc/PROFANCY.pdf
inst/doc/PROFANCY.Rnw
inst/localdata
inst/localdata/ProstateSeeds.txt
inst/localdata/ProstateCandidates.txt
DESCRIPTION
data
data/envData.rda
data/datalist
PROFANCY documentation built on May 19, 2017, 10:34 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.