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.

Author
UnJin Lee
Date of publication
None
Maintainer
UnJin Lee <unjin@uchicago.edu>
License
GPL version 3
Version
1.6.0

View on Bioconductor

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

Files in this package

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