SIMMS: Subnetwork Integration for Multi-Modal Signatures

Algorithms to create prognostic biomarkers using biological networks.

Install the latest version of this package by entering the following in R:
install.packages("SIMMS")
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

View on CRAN

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

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.