SIMMS (version 1.3.2)

Subnetwork Integration for Multi-Modal Signatures

Description

Algorithms to create prognostic biomarkers using biological genesets or networks.

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Version

Install

install.packages('SIMMS')

Monthly Downloads

218

Version

1.3.2

License

GPL-2

Maintainer

Syed Haider

Last Published

April 24th, 2022

Functions in SIMMS (1.3.2)

fit.coxmodel

Fit a Cox proportional hazards model

fit.interaction.model

Cox model two features separately and together

SIMMS-package

SIMMS - Subnetwork Integration for Multi-Modal Signatures

calculate.meta.survival

Fit a meta-analytic Cox proportional hazards model to a single feature

centre.scale.dataset

Centre and scale a data matrix

get.chisq.stats

Applies survdiff function

create.KM.plot

Plots Kaplan-meier survival curve for a given risk grouping & survival params

get.program.defaults

A utility function to return the inst/ directory of the installed package and other default settings

create.sensitivity.plot

Plots sensitivity analysis for class label dichotomization at supplied survtime cutoffs

create.survivalplots

Plots Kaplan-meier survival curves

dichotomize.dataset

Dichotomize a single dataset

dichotomize.meta.dataset

Dichotomize and unlist a meta-analysis list

create.survobj

Utility function for loading meta-analysis lists

derive.network.features

Derive univariate features from pathway-derived networks

load.cancer.datasets

Load all cancer meta-analysis datasets

create.classifier.multivariate

Trains and tests a multivariate survival model

create.classifier.univariate

Trains and tests a univariate (per subnetwork module) survival model

prepare.training.validation.datasets

Prepare training and validation datasets

pred.survivalmodel

Apply a multivariate survival model to validation datasets

calculate.network.coefficients

Calculate Cox statistics for input dataset

calculate.sensitivity.stats

Computes sensitivity measures

fit.survivalmodel

Trains a multivariate survival model

get.adjacency.matrix

A utility function to convert tab delimited networks file into adjacency matrices

make.matrix

Utility function used by get.adjacency.matrix()