SIMMS: Subnetwork Integration for Multi-Modal Signatures
Version 1.0.2

Algorithms to create prognostic biomarkers using biological networks.

Browse man pages Browse package API and functions Browse package files

AuthorSyed Haider, Michal Grzadkowski, Paul C. Boutros
Date of publication2015-09-21 17:57:55
MaintainerSyed Haider <Syed.Haider@oicr.on.ca>
LicenseGPL-2
Version1.0.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SIMMS")

Man pages

calculate.meta.survival: Fit a meta-analytic Cox proportional hazards model to a...
calculate.network.coefficients: Calculate Cox statistics for input dataset
calculate.sensitivity.stats: Computes sensitivity measures
create.classifier.multivariate: Trains and tests a multivariate survival model
create.classifier.univariate: Trains and tests a univariate (per subnetwork module)...
create.KM.plot: Plots Kaplan-meier survival curve for a given risk grouping &...
create.sensitivity.plot: Plots sensitivity analysis for class label dichotomization at...
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...
get.chisq.stats: Applies survdiff function
get.program.defaults: A utility function to return the inst/ directory of the...
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

Functions

SIMMS Man page
SIMMS-package Man page
calculate.meta.survival Man page Source code
calculate.network.coefficients Man page Source code
calculate.sensitivity.stats Man page Source code
create.KM.plot Man page Source code
create.classifier.multivariate Man page Source code
create.classifier.univariate Man page Source code
create.sensitivity.plot Man page Source code
create.survivalplots Man page Source code
create.survobj Man page Source code
derive.network.features Man page Source code
dichotomize.dataset Man page Source code
dichotomize.meta.dataset Man page Source code
fit.coxmodel Man page Source code
fit.interaction.model Man page Source code
fit.survivalmodel Man page Source code
get.adjacency.matrix Man page Source code
get.chisq.stats Man page Source code
get.program.defaults Man page Source code
load.cancer.datasets Man page Source code
make.matrix Man page Source code
pred.survivalmodel Man page Source code
prepare.training.validation.datasets Man page Source code

Files

inst
inst/programdata
inst/programdata/networkdb
inst/programdata/networkdb/MEMo.BRCA
inst/programdata/networkdb/MEMo.BRCA/pathway_based_sub_networks.txt
inst/programdata/networkdb/MEMo.BRCA/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/MEMo.BRCA/pathway_based_networks_flattened.txt
inst/programdata/networkdb/Mammaprint
inst/programdata/networkdb/Mammaprint/pathway_based_sub_networks.txt
inst/programdata/networkdb/Mammaprint/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/Mammaprint/pathway_based_networks_flattened.txt
inst/programdata/networkdb/Oncotypedx
inst/programdata/networkdb/Oncotypedx/pathway_based_sub_networks.txt
inst/programdata/networkdb/Oncotypedx/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/Oncotypedx/pathway_based_networks_flattened.txt
inst/programdata/networkdb/PI3K
inst/programdata/networkdb/PI3K/pathway_based_sub_networks.txt
inst/programdata/networkdb/PI3K/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/PI3K/pathway_based_networks_flattened.txt
inst/programdata/networkdb/MEMo
inst/programdata/networkdb/MEMo/HGNC_Entrez_map.txt
inst/programdata/networkdb/MEMo/pathway_based_sub_networks__HGNC.txt
inst/programdata/networkdb/MEMo/pathway_based_sub_networks.txt
inst/programdata/networkdb/MEMo/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/MEMo/map.hgnc.entrez.R
inst/programdata/networkdb/MEMo/pathway_based_networks_flattened.txt
inst/programdata/networkdb/HiC.gm06690
inst/programdata/networkdb/HiC.gm06690/pathway_based_sub_networks.txt
inst/programdata/networkdb/HiC.gm06690/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/HiC.gm06690/pathway_based_networks_flattened.txt
inst/programdata/networkdb/MEMo.GBM
inst/programdata/networkdb/MEMo.GBM/pathway_based_sub_networks.txt
inst/programdata/networkdb/MEMo.GBM/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/MEMo.GBM/pathway_based_networks_flattened.txt
inst/programdata/networkdb/default
inst/programdata/networkdb/default/pathway_based_sub_networks.txt
inst/programdata/networkdb/default/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/default/pathway_based_networks.txt
inst/programdata/networkdb/default/pathway_based_networks_flattened.txt
inst/programdata/networkdb/test
inst/programdata/networkdb/test/pathway_based_sub_networks.txt
inst/programdata/networkdb/test/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/test/pathway_based_networks_flattened.txt
inst/programdata/networkdb/MEMo.KIRC
inst/programdata/networkdb/MEMo.KIRC/pathway_based_sub_networks.txt
inst/programdata/networkdb/MEMo.KIRC/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/MEMo.KIRC/pathway_based_networks_flattened.txt
inst/programdata/networkdb/MEMo.OV
inst/programdata/networkdb/MEMo.OV/pathway_based_sub_networks.txt
inst/programdata/networkdb/MEMo.OV/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/MEMo.OV/pathway_based_networks_flattened.txt
inst/programdata/networkdb/MEMo.COADREAD
inst/programdata/networkdb/MEMo.COADREAD/pathway_based_sub_networks.txt
inst/programdata/networkdb/MEMo.COADREAD/pathway_based_sub_networks_all.txt
inst/programdata/networkdb/MEMo.COADREAD/pathway_based_networks_flattened.txt
inst/programdata/testdata
inst/programdata/testdata/datasets.txt
inst/programdata/testdata/Breastdata1
inst/programdata/testdata/Breastdata1/patient_annotation.txt
inst/programdata/testdata/Breastdata1/mRNA_abundance.txt
inst/programdata/testdata/Breastdata2
inst/programdata/testdata/Breastdata2/patient_annotation.txt
inst/programdata/testdata/Breastdata2/mRNA_abundance.txt
inst/doc
inst/doc/Using-SIMMS.R
inst/doc/Using-SIMMS.html
inst/doc/Using-SIMMS.Rmd
NAMESPACE
NEWS
R
R/get.chisq.stats.R
R/get.program.defaults.R
R/create.KM.plot.R
R/calculate.meta.survival.R
R/fit.survivalmodel.R
R/calculate.sensitivity.stats.R
R/make.matrix.R
R/fit.interaction.model.R
R/calculate.network.coefficients.R
R/fit.coxmodel.R
R/load.cancer.datasets.R
R/dichotomize.dataset.R
R/get.adjacency.matrix.R
R/derive.network.features.R
R/create.survobj.R
R/dichotomize.meta.dataset.R
R/create.sensitivity.plot.R
R/create.classifier.multivariate.R
R/pred.survivalmodel.R
R/prepare.training.validation.datasets.R
R/create.survivalplots.R
R/create.classifier.univariate.R
vignettes
vignettes/GitHub2.css
vignettes/Using-SIMMS.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/dichotomize.meta.dataset.Rd
man/get.adjacency.matrix.Rd
man/make.matrix.Rd
man/prepare.training.validation.datasets.Rd
man/create.KM.plot.Rd
man/derive.network.features.Rd
man/create.sensitivity.plot.Rd
man/calculate.network.coefficients.Rd
man/load.cancer.datasets.Rd
man/create.survobj.Rd
man/get.program.defaults.Rd
man/fit.coxmodel.Rd
man/pred.survivalmodel.Rd
man/fit.interaction.model.Rd
man/create.classifier.multivariate.Rd
man/SIMMS.Rd
man/fit.survivalmodel.Rd
man/create.classifier.univariate.Rd
man/dichotomize.dataset.Rd
man/create.survivalplots.Rd
man/get.chisq.stats.Rd
man/calculate.sensitivity.stats.Rd
man/calculate.meta.survival.Rd
SIMMS documentation built on May 19, 2017, 6:47 p.m.