SIMMS: Subnetwork Integration for Multi-Modal Signatures

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Algorithms to create prognostic biomarkers using biological networks.

Author
Syed Haider, Michal Grzadkowski, Paul C. Boutros
Date of publication
2015-09-21 17:57:55
Maintainer
Syed Haider <Syed.Haider@oicr.on.ca>
License
GPL-2
Version
1.0.2

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

Files in this package

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