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 |