Subnetwork Integration for Multi-Modal Signatures
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Documentation for package ‘SIMMS’ version 1.3.2
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 |