sigCheckKnown: Check signature performance against a panel of known...

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/sigCheckKnown.R

Description

Performance of a signature is compared to performance of a panel of known (previously identified) signature.

Usage

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sigCheckKnown(check, known="cancer")

Arguments

check

A SigCheckObject, as returned by sigCheck.

known

Either a character string specifying which set of signatures to use from the included sets in knownSignatures, or a list of previously identified signatures to compare performance against. Each element in the list should be a vector of feature labels. Default is to use the "cancer" signatures from the included k knownSignatures data set, taken from Venet et. al.

Details

Each specified known signature will be evaluated in the same manner as the primary signature. If survival data were supplied, a survival analysis will be carried out on the validation samples, and a p-value computed as a performance measure. If no survival data are available, the training samples will be used to train a classifier, and the performance score will be percentage of validation samples correctly classified. (If no validation samples are provided, leave-one-out cross validation will be used to calculate the classification performance for each known signature).

An empirical p-value will be computed based on the percentile rank of the performance of the primary signature compared to a null distribution of the performance of the known signatures.

Value

A result list with the following elements:

Author(s)

Rory Stark

References

Venet, David, Jacques E. Dumont, and Vincent Detours. "Most random gene expression signatures are significantly associated with breast cancer outcome." PLoS Computational Biology 7.10 (2011): e1002240.

See Also

knownSignatures, sigCheck, sigCheckAll, sigCheckRandom, sigCheckPermuted, sigCheckPlot

Examples

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#Disable parallel so Bioconductor build won't hang
library(BiocParallel)
register(SerialParam())

library(breastCancerNKI)
data(nki)
nki <- nki[,!is.na(nki$e.dmfs)]
data(knownSignatures)

## survival analysis
check <- sigCheck(nki, classes="e.dmfs", survival="t.dmfs",
                  signature=knownSignatures$cancer$VANTVEER,
                  annotation="HUGO.gene.symbol",
                  validationSamples=150:319)

knownResult <- sigCheckKnown(check)
knownResult$checkPval
knownResult$survivalPvalsKnown[knownResult$survivalPvalsKnown <
                               knownResult$checkPval]
sigCheckPlot(knownResult)

SigCheck documentation built on May 6, 2019, 3:01 a.m.