R: Subnetwork Integration for Multi-Modal Signatures

# Subnetwork Integration for Multi-Modal Signatures

## Documentation for package ‘SIMMS’ version 1.3.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

SIMMS-package | SIMMS - Subnetwork Integration for Multi-Modal Signatures
calculate.meta.survival | Fit a meta-analytic Cox proportional hazards model to a single feature
calculate.network.coefficients | Calculate Cox statistics for input dataset
calculate.sensitivity.stats | Computes sensitivity measures
centre.scale.dataset | Centre and scale a data matrix
create.classifier.multivariate | Trains and tests a multivariate survival model
create.classifier.univariate | Trains and tests a univariate (per subnetwork module) survival model
create.KM.plot | Plots Kaplan-meier survival curve for a given risk grouping & survival params
create.sensitivity.plot | Plots sensitivity analysis for class label dichotomization at supplied survtime cutoffs
create.survivalplots | Plots Kaplan-meier survival curves
create.survobj | Utility function for loading meta-analysis lists
derive.network.features | Derive univariate features from pathway-derived networks
dichotomize.dataset | Dichotomize a single dataset
dichotomize.meta.dataset | Dichotomize and unlist a meta-analysis list
fit.coxmodel | Fit a Cox proportional hazards model
fit.interaction.model | Cox model two features separately and together
fit.survivalmodel | Trains a multivariate survival model
get.adjacency.matrix | A utility function to convert tab delimited networks file into adjacency matrices
get.chisq.stats | Applies survdiff function
get.program.defaults | A utility function to return the inst/ directory of the installed package and other default settings
load.cancer.datasets | Load all cancer meta-analysis datasets
make.matrix | Utility function used by 'get.adjacency.matrix()'
pred.survivalmodel | Apply a multivariate survival model to validation datasets
prepare.training.validation.datasets | Prepare training and validation datasets
SIMMS | SIMMS - Subnetwork Integration for Multi-Modal Signatures