Package: SigCheck 2.45.0

Rory Stark

SigCheck: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

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.

Authors:Rory Stark <[email protected]> and Justin Norden

SigCheck_2.45.0.tar.gz
SigCheck_2.45.0.zip(r-4.7)SigCheck_2.45.0.zip(r-4.6)SigCheck_2.45.0.zip(r-4.5)
SigCheck_2.45.0.tgz(r-4.6-any)SigCheck_2.45.0.tgz(r-4.5-any)
SigCheck_2.45.0.tar.gz(r-4.7-any)SigCheck_2.45.0.tar.gz(r-4.6-any)
SigCheck_2.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SigCheck/json (API)

# Install 'SigCheck' in R:

install.packages('SigCheck', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

knownSignatures - Previously identified gene signatures for use in 'sigCheckKnown'
nkiResults - Precomputed list of results for a call to 'sigCheckAll' using the 'breastCancerNKI' dataset.

On BioConductor:SigCheck-2.45.0(bioc 3.24)SigCheck-2.44.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression classification genesetenrichment

3.30 score 2 scripts 388 downloads 1 mentions 6 exports 121 dependencies

Last updated from:0a23557023. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	234
linux-devel-x86_64	NOTE	514
source / vignettes	OK	419
linux-release-x86_64	NOTE	515
macos-release-arm64	NOTE	367
macos-oldrel-arm64	NOTE	366
windows-devel	NOTE	404
windows-release	NOTE	387
windows-oldrel	NOTE	405
wasm-release	OK	206

Exports:sigCheck sigCheckAll sigCheckKnown sigCheckPermuted sigCheckPlot sigCheckRandom

Dependencies:abind annotate AnnotationDbi askpass assertthat base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob bslib cachem class cli cluster codetools commonmark cpp11 crayon crosstalk curl DBI DelayedArray DEoptimR digest diptest dplyr e1071 evaluate fastmap flexmix fontawesome formatR fpc fs futile.logger futile.options gbm gdata genefilter generics GenomicRanges ggvis glue gtools highr htmltools htmlwidgets httpuv httr hwriter igraph IRanges jquerylib jsonlite KEGGREST kernlab knitr lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime mlbench MLInterfaces modeltools nnet openssl otel pillar pkgconfig pls png prabclus promises proxy R6 rappdirs RColorBrewer Rcpp rlang rmarkdown robustbase rpart RSQLite S4Arrays S4Vectors sass Seqinfo sfsmisc shiny snow sourcetools SparseArray SummarizedExperiment survival sys threejs tibble tidyselect tinytex utf8 vctrs withr xfun XML xtable XVector yaml

Checking gene expression signatures against random and known signatures with SigCheck

Rendered fromSigCheck.Rnwusingutils::Sweave

Last update: 2025-02-14
Started: 2022-12-09

Help page	Topics
Check a gene signature's survival and/or classification performance against random signatures, known signatures, and permuted data/metadata.	SigCheck-package SigCheck
Precomputed list of results for a calls to 'sigCheckRandom' and 'sigCheckKnown' using the 'breastCancerNKI' dataset.	classifyResults
Previously identified gene signatures for use in 'sigCheckKnown'	knownSignatures resultsNKI
Precomputed list of results for a call to 'sigCheckAll' using the 'breastCancerNKI' dataset.	nkiResults
Create a 'SigCheckObject' and establish baseline performance.	sigCheck
Run a default set of checks on a gene signature.	sigCheckAll
Check signature performance against a panel of known signatures.	sigCheckKnown
Class '"SigCheckObject"'	SigCheckObject SigCheckObject-class
Check signature performance against performance on randomly permuted data.	sigCheckPermuted
Plot results of a signature check or set of checks	sigCheckPlot
Check signature performance against signatures composed of randomly selected features	sigCheckRandom

Package: SigCheck 2.45.0

SigCheck: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

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