netprioR-class: netprioR

In cbg-ethz/netprioR: A model for network-based prioritisation of genes

Description

Class that represents a netprioR model.

Usage

netprioR(networks, phenotypes, labels, ...)

## S4 method for signature 'list,matrix,factor'
netprioR(networks, phenotypes, labels,
  fit.model = FALSE, a = 0.1, b = 0.1, sigma2 = 0.1, tau2 = 100,
  eps = 1e-10, max.iter = 500, thresh = 1e-06, use.cg = FALSE,
  thresh.cg = 1e-06, nrestarts = 5, max.cores = detectCores(),
  verbose = TRUE, ...)

Arguments

networks	List of NxN adjacency matrices of gene-gene similarities
phenotypes	Matrix of dimension NxP containing covariates
labels	Vector of Nx1 labels for all genes (NA if no label available)
...	Additional arguments
fit.model	Indicator whether to fit the model
a	Shape parameter of Gamma prior for W
b	Scale parameter of Gamma prior for W
sigma2	Cariance for Gaussian labels
tau2	Variance for Gaussian prior for beta
eps	Small value added to diagonal of Q in order to make it non-singular
max.iter	Maximum number of iterations for EM
thresh	Threshold for termination of EM with respect to change in parameters
use.cg	Flag whether to use conjugate gradient instead of exact computation of expectations
thresh.cg	Threshold for the termination of the conjugate gradient solver
nrestarts	Number of restarts for EM
max.cores	Maximum number of cores to use for parallel computation
verbose	Print verbose output

Value

A netprioR object

Slots

networks

List of NxN adjacency matrices of gene-gene similarities

phenotypes

Matrix of dimension NxP containing covariates

labels

Vector of Nx1 labels for all genes. NA if no label available.

is.fitted

Flag indicating if model is fitted

model

List containing estimated parameters and imputed missing data

Author(s)

Fabian Schmich

Examples

 # runs long-ish
data(simulation)
np <- netprioR(networks = simulation$networks,
               phenotypes = simulation$phenotypes,
               labels = simulation$labels.obs,
               fit.model = TRUE)
summary(np)          

cbg-ethz/netprioR documentation built on May 13, 2019, 2:02 p.m.