SigCheck
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Bioconductor version: 3.23 · Package version: 2.44.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
While gene signatures are frequently used to predict phenotypes (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours' paper "Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome"). Based on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SigCheck")Details
| Maintainer | Rory Stark <bioconductor@starkhome.com> |
| Author | Rory Stark <bioconductor@starkhome.com> and Justin Norden |
| License | Artistic-2.0 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, GeneExpression, GeneSetEnrichment, Software |
| Package Short Url | https://bioconductor.org/packages/SigCheck/ |
Citation
From within R, enter citation("SigCheck"):
Rory Stark and Justin Norden. SigCheck: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata. doi:10.18129/B9.bioc.SigCheck, R package version 2.44.0, https://bioconductor.org/packages/SigCheck.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SigCheck_2.44.0.tar.gz |
| Windows binary (x86_64) | SigCheck_2.44.0.zip |
| macOS binary (arm64) | SigCheck_2.44.0.tgz |
| macOS binary (x86_64) | SigCheck_2.44.0.tgz |
Dependencies
Depends: R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel, survival
Imports: graphics, stats, utils, methods
Suggests: BiocStyle, breastCancerNKI, qusage