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

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.

Author
Qianlan Yao, Desi Shang, Chunquan Li
Date of publication
2013-07-12 08:58:53
Maintainer
Qianlan Yao <yaoqianlan@yahoo.com>
License
GPL (>= 2)
Version
1.0

View on CRAN

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

Files in this package

PROFANCY
PROFANCY/MD5
PROFANCY/NAMESPACE
PROFANCY/vignettes
PROFANCY/vignettes/PROFANCY.Rnw
PROFANCY/R
PROFANCY/R/getTopDiseaseMetaboliteList.R
PROFANCY/man
PROFANCY/man/PROFANCY-internal.Rd
PROFANCY/man/initializeData.Rd
PROFANCY/man/getTopDiseaseMetabolites.Rd
PROFANCY/man/getSeed.Rd
PROFANCY/man/getProvidedDiseaseName.Rd
PROFANCY/man/getCandidates.Rd
PROFANCY/man/envData.Rd
PROFANCY/man/aaa-PROFANCY-package.Rd
PROFANCY/inst
PROFANCY/inst/doc
PROFANCY/inst/doc/PROFANCY.pdf
PROFANCY/inst/doc/PROFANCY.Rnw
PROFANCY/inst/localdata
PROFANCY/inst/localdata/ProstateSeeds.txt
PROFANCY/inst/localdata/ProstateCandidates.txt
PROFANCY/DESCRIPTION
PROFANCY/data
PROFANCY/data/envData.rda
PROFANCY/data/datalist