netgsa: Network-Based Gene Set Analysis
Version 3.0

Carry out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data.

Browse man pages Browse package API and functions Browse package files

AuthorAli Shojaie and Jing Ma
Date of publication2016-06-16 18:27:48
MaintainerJing Ma <jinma@upenn.edu>
LicenseGPL (>= 2)
Version3.0
URL http://arxiv.org/abs/1411.7919
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("netgsa")

Man pages

bic.netEst.undir: Bayesian information criterion to select the tuning...
edgelist: An example edge list
edgelist2adj: Construct an adjacency matrix from an edge list
netEst.dir: Constrained estimation of directed networks
netEst.undir: Constrained estimation of undirected networks
NetGSA: Network-based Gene Set Analysis
netgsaex2: Toy example for using 'NetGSA' on a two-class test with...
netgsaex3: Toy example for using 'NetGSA' on a three-class test with...
netgsaexDAG: Toy example for using 'NetGSA' on a two-class test with...
netgsa-package: Network-Based Gene Set Analysis
nonedgelist: An example for not-an-edge list

Functions

NetGSA Man page Source code
adj2inf Source code
approxVarEst Source code
bic.netEst.undir Man page Source code
call.netgsa Source code
edgelist Man page
edgelist2adj Man page Source code
get.contrast Source code
glmnet.soft Source code
graphlaplacian Source code
matTr Source code
netEst.dir Man page Source code
netEst.undir Man page Source code
netgsa-package Man page Man page
netgsa.ftest Source code
netgsa.ttest Source code
netgsaex2 Man page
netgsaex3 Man page
netgsaexDAG Man page
newton Source code
nonedgelist Man page
normalizeAdj Source code
profile.newton.se Source code
zeroInd Source code

Files

NAMESPACE
data
data/netgsaexDAG.rda
data/netgsaex2.rda
data/netgsaex3.rda
data/nonedgelist.rda
data/edgelist.rda
R
R/profile.newton.se.R
R/NetGSA.R
R/normalizeAdj.R
R/zeroInd.R
R/glmnet.soft.R
R/netgsa.ttest.R
R/netgsa.ftest.R
R/get.contrast.R
R/call.netgsa.R
R/edgelist2adj.R
R/matTr.R
R/newton.R
R/netEst.undir.R
R/adj2inf.R
R/bic.netEst.undir.R
R/graphlaplacian.R
R/netEst.dir.R
R/approxVarEst.R
R/netgsa-internal.R
MD5
DESCRIPTION
man
man/bic.netEst.undir.Rd
man/nonedgelist.Rd
man/netgsaexDAG.Rd
man/NetGSA.Rd
man/edgelist2adj.Rd
man/netEst.dir.Rd
man/netgsa-package.Rd
man/netgsaex2.Rd
man/netgsaex3.Rd
man/netEst.undir.Rd
man/edgelist.Rd
netgsa documentation built on May 19, 2017, 11:48 p.m.