sigsquared: Gene signature generation for functionally validated signaling pathways

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.

AuthorUnJin Lee
Date of publicationNone
MaintainerUnJin Lee <unjin@uchicago.edu>
LicenseGPL version 3
Version1.6.0

View on Bioconductor

Functions

analysisPipeline Man page
analysisPipeline,ExpressionSet,geneSignature-method Man page
BrCa443 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
setGenes Man page
setGenes,geneSignature-method Man page
setGeneSignature Man page
setGeneSignature,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

sigsquared/DESCRIPTION
sigsquared/NAMESPACE
sigsquared/R
sigsquared/R/GeneSignature.R sigsquared/R/SolnSpace.R
sigsquared/build
sigsquared/build/vignette.rds
sigsquared/data
sigsquared/data/BrCa443.RData
sigsquared/inst
sigsquared/inst/doc
sigsquared/inst/doc/sigsquared.R
sigsquared/inst/doc/sigsquared.Rnw
sigsquared/inst/doc/sigsquared.pdf
sigsquared/inst/unitTests
sigsquared/inst/unitTests/test_ensembleAdjustable.R
sigsquared/inst/unitTests/test_geneSignaturehelpers.R
sigsquared/man
sigsquared/man/BrCa443.Rd sigsquared/man/analysisPipeline.Rd sigsquared/man/ensembleAdjustable.Rd sigsquared/man/geneSignature-class.Rd sigsquared/man/setGeneSignature.Rd sigsquared/man/sigsquared.Rd
sigsquared/tests
sigsquared/tests/runTests.R
sigsquared/vignettes
sigsquared/vignettes/bpmsnetwork.png
sigsquared/vignettes/sigsquared.Rnw

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

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