netprioR: A model for network-based prioritisation of genes
Version 1.2.0

A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.

Browse man pages Browse package API and functions Browse package files

AuthorFabian Schmich
Bioconductor views CellBasedAssays Network Preprocessing
Date of publicationNone
MaintainerFabian Schmich <fabian.schmich@bsse.ethz.ch>
LicenseGPL-3
Version1.2.0
URL http://bioconductor.org/packages/netprioR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("netprioR")

Man pages

bandwidth: bandwidth
cmn: Class Mass Normalization (CMN) from Zhu et al., 2003
conjugate_gradient: Conjugate Gradient Solver
cuthill_mckee: Cuthill McKee (CM) algorithm
fit-methods: Fit 'netprioR' model
laplacian: Graph Laplacian
learn: Fit netprioR model
netprioR-class: netprioR
netprioR-package: Package: netprioR
norm_kern: Normalise kernel
plot.netprioR: Plot method for 'netprioR' objects
ranks-methods: Retrieve ranked prioritisation list
ROC-methods: Compute ROC curve from netprioR model and true labels
simulate_labels: Simulate labels
simulate_network_random: Simulate random networks with predefined number of members...
simulate_network_scalefree: Simulate scalefree networks
simulate_phenotype: Simulate phenotypes correlated to labels pivoted into two...
simulation: Example data: Simulated networks, phenotypes and labels for N...
weights-methods: Retrieve network weights

Functions

ROC Man page
ROC,netprioR-method Man page
bandwidth Man page Source code
cmn Man page Source code
conjugate_gradient Man page Source code
cuthill_mckee Man page Source code
fit Man page
fit,netprioR-method Man page
laplacian Man page Source code
learn Man page Source code
netprioR Man page
netprioR,list,matrix,factor-method Man page
netprioR-class Man page
netprioR-package Man page
norm_kern Man page Source code
plot.netprioR Man page Source code
ranks Man page
ranks,netprioR-method Man page
simulate_labels Man page Source code
simulate_network_random Man page Source code
simulate_network_scalefree Man page Source code
simulate_phenotype Man page Source code
simulation Man page
weights Man page
weights,netprioR-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/netprioR-class.R
R/netprioR-functions.R
R/netprioR-generics.R
R/netprioR-methods.R
R/netprioR-package.R
R/netprioR-simulation.R
README.md
build
build/vignette.rds
data
data/simulation.rdata
inst
inst/NEWS
inst/doc
inst/doc/netprioR.R
inst/doc/netprioR.Rmd
inst/doc/netprioR.html
inst/example
inst/example/data_simulation.R
man
man/ROC-methods.Rd
man/bandwidth.Rd
man/cmn.Rd
man/conjugate_gradient.Rd
man/cuthill_mckee.Rd
man/fit-methods.Rd
man/laplacian.Rd
man/learn.Rd
man/netprioR-class.Rd
man/netprioR-package.Rd
man/norm_kern.Rd
man/plot.netprioR.Rd
man/ranks-methods.Rd
man/simulate_labels.Rd
man/simulate_network_random.Rd
man/simulate_network_scalefree.Rd
man/simulate_phenotype.Rd
man/simulation.Rd
man/weights-methods.Rd
vignettes
vignettes/netprioR.Rmd
netprioR documentation built on May 20, 2017, 9:56 p.m.