SIMMS: Subnetwork Integration for Multi-Modal Signatures

Algorithms to create prognostic biomarkers using biological networks.

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

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

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.