Package: sigsquared 1.39.0
UnJin Lee
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.
Authors:
sigsquared_1.39.0.tar.gz
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sigsquared.pdf |sigsquared.html✨
sigsquared/json (API)
| # Install 'sigsquared' in R: |
| install.packages('sigsquared', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- BrCa443 - Breast Cancer 443 Data Set
On BioConductor:sigsquared-1.39.0(bioc 3.21)sigsquared-1.38.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:1fece7e65b. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | NOTE | Dec 18 2024 |
| R-4.5-linux | NOTE | Dec 18 2024 |
| R-4.4-win | NOTE | Dec 18 2024 |
| R-4.4-mac | NOTE | Dec 18 2024 |
| R-4.3-win | NOTE | Dec 18 2024 |
| R-4.3-mac | NOTE | Dec 18 2024 |
Exports:analysisPipelineensembleAdjustablegetDirectgetGenesgetNGenesgetThresholdssetDirectsetGenessetGeneSignaturesetThresholds
Dependencies:BiobaseBiocGenericsgenericslatticeMatrixsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Training of thresholds | analysisPipeline |
| Breast Cancer 443 Data Set | BrCa443 |
| Application of geneSignature object | ensembleAdjustable |
| Class '"geneSignature"' | analysisPipeline,ExpressionSet,geneSignature-method ensembleAdjustable,ExpressionSet,geneSignature-method ensembleAdjustable,matrix,geneSignature-method geneSignature-class getDirect,geneSignature-method getGenes,geneSignature-method getGenes,solnSpace-method getNGenes,geneSignature-method getThresholds,geneSignature-method getThresholds,solnSpace-method setDirect,geneSignature,numeric-method setGenes,geneSignature-method setGenes,solnSpace-method setGeneSignature,geneSignature-method setThresholds,geneSignature-method setThresholds,solnSpace-method |
| geneSignature functions | getDirect getGenes getNGenes getThresholds setDirect setGenes setGeneSignature setThresholds |
| The sigsquared package | sigsquared |
