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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.
● Data Source:
BioConductor
● Keywords: package
● Alias: SigCheck, SigCheck-package
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The main object containing everything associated with an expression dataset and a gene signatures. Used for subsequent checks of the unique prognostic and/or classification performance of the signature. Based on an ExpressionSet object.
● Data Source:
BioConductor
● Keywords: classes
● Alias: SigCheckObject, SigCheckObject-class
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Main constructor for a SigCheckObject. Also establishes baseline survival analysis and/or classification performance.
● Data Source:
BioConductor
● Keywords:
● Alias: sigCheck
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High-level function for package SigCheck that runs a default set of checks against a predictive signature.
● Data Source:
BioConductor
● Keywords:
● Alias: sigCheckAll
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Performance of a signature is compared to performance of a panel of known (previously identified) signature.
● Data Source:
BioConductor
● Keywords:
● Alias: sigCheckKnown
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Performance of a signature on intact data is compared to performance on permuted data and/or metadata. Data may be permuted by by feature (expression values of each feature permuted across samples), samples (expression values of all features permuted within each sample). Metadata may be permuted by categories (permuted assignment of samples to classification categories) or survival (permuted assignment of survival times to samples).
● Data Source:
BioConductor
● Keywords:
● Alias: sigCheckPermuted
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Plots results of a signature check, as returned by sigCheckRandom, sigCheckKnown, sigCheckPermuted, or sigCheckAll.
● Data Source:
BioConductor
● Keywords:
● Alias: sigCheckPlot
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Performance of a signature is compared to performance of signatures composed of the same number of randomly-selected features.
● Data Source:
BioConductor
● Keywords:
● Alias: sigCheckRandom
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providing 
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