DRaWR: Discriminative Random Walk with Restart

We present DRaWR, a network-based method for ranking genes or properties related to a given gene set. Such related genes or properties are identified from among the nodes of a large, heterogeneous network of biological information. Our method involves a random walk with restarts, performed on an initial network with multiple node and edge types, preserving more of the original, specific property information than current methods that operate on homogeneous networks. In this first stage of our algorithm, we find the properties that are the most relevant to the given gene set and extract a subnetwork of the original network, comprising only the relevant properties. We then rerank genes by their similarity to the given gene set, based on a second random walk with restarts, performed on the above subnetwork.

Author
Charles Blatti [aut, cre]
Date of publication
2016-02-05 00:55:30
Maintainer
Charles Blatti <blatti@illinois.edu>
License
GPL-2
Version
1.0.1

View on CRAN

Man pages

DRaWR
DRaWR
RWR
RWR
threeCol2listMat
threeCol2listMat
threeCol2MaxMat
threeCol2MaxMat
transmat
Sample transition matrix.

Files in this package

DRaWR
DRaWR/inst
DRaWR/inst/extdata
DRaWR/inst/extdata/sample.setlist
DRaWR/inst/extdata/sample.uni
DRaWR/inst/extdata/output_sample.uni.sample.undir.weight.type.50.1e-04.1.1.0.7.sample.query.1.rwr
DRaWR/inst/extdata/sample.query
DRaWR/inst/extdata/output_sample.uni.sample.undir.weight.type.50.1e-04.0.7.base
DRaWR/inst/extdata/output_sample.uni.sample.undir.weight.type.50.1e-04.1.1.0.7.sample.setlist.stats
DRaWR/inst/extdata/sample.edge
DRaWR/NAMESPACE
DRaWR/data
DRaWR/data/transmat.RData
DRaWR/R
DRaWR/R/DRaWR.R
DRaWR/MD5
DRaWR/DESCRIPTION
DRaWR/man
DRaWR/man/RWR.Rd
DRaWR/man/threeCol2listMat.Rd
DRaWR/man/transmat.Rd
DRaWR/man/threeCol2MaxMat.Rd
DRaWR/man/DRaWR.Rd