sigsquared: Gene signature generation for functionally validated signaling pathways
Version 1.8.0

By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.

Browse man pages Browse package API and functions Browse package files

AuthorUnJin Lee
Date of publicationNone
MaintainerUnJin Lee <unjin@uchicago.edu>
LicenseGPL version 3
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sigsquared")

Man pages

analysisPipeline: Training of thresholds
BrCa443: Breast Cancer 443 Data Set
ensembleAdjustable: Application of geneSignature object
geneSignature-class: Class '"geneSignature"'
setGeneSignature: geneSignature functions
sigsquared: The sigsquared package

Functions

BrCa443 Man page
analysisPipeline Man page
analysisPipeline,ExpressionSet,geneSignature-method Man page
ensembleAdjustable Man page
ensembleAdjustable,ExpressionSet,geneSignature-method Man page
ensembleAdjustable,matrix,geneSignature-method Man page
geneSignature-class Man page
getDirect Man page
getDirect,geneSignature-method Man page
getGenes Man page
getGenes,geneSignature-method Man page
getGenes,solnSpace-method Man page
getNGenes Man page
getNGenes,geneSignature-method Man page
getThresholds Man page
getThresholds,geneSignature-method Man page
getThresholds,solnSpace-method Man page
setDirect Man page
setDirect,geneSignature,numeric-method Man page
setGeneSignature Man page
setGeneSignature,geneSignature-method Man page
setGenes Man page
setGenes,geneSignature-method Man page
setGenes,solnSpace-method Man page
setThresholds Man page
setThresholds,geneSignature-method Man page
setThresholds,solnSpace-method Man page
sigsquared Man page

Files

DESCRIPTION
NAMESPACE
R
R/GeneSignature.R
R/SolnSpace.R
build
build/vignette.rds
data
data/BrCa443.RData
inst
inst/doc
inst/doc/sigsquared.R
inst/doc/sigsquared.Rnw
inst/doc/sigsquared.pdf
inst/unitTests
inst/unitTests/test_ensembleAdjustable.R
inst/unitTests/test_geneSignaturehelpers.R
man
man/BrCa443.Rd
man/analysisPipeline.Rd
man/ensembleAdjustable.Rd
man/geneSignature-class.Rd
man/setGeneSignature.Rd
man/sigsquared.Rd
tests
tests/runTests.R
vignettes
vignettes/bpmsnetwork.png
vignettes/sigsquared.Rnw
sigsquared documentation built on May 20, 2017, 10:31 p.m.