sigCheckPermuted: Check signature performance against performance on randomly...

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

View source: R/sigCheckPermuted.R

Description

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).

Usage

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sigCheckPermuted(check, toPermute="categories", iterations=10)

Arguments

check

A SigCheckObject, as returned by sigCheck.

toPermute

Character string or vector of strings indicating what should be permuted. Allowable values:

  • "features": the expression values for each feature will be permuted (permutation by row).

  • "samples": the expression values for each sample will be permuted (permutation by column).

  • "survival": the values in survival will be permuted.

  • "categories": the values in classes will be permuted.

iterations

The number of permuted dataset the primary signature will be compared to. This should be at least 1,000 to compute a meaningful empirical p-value for comparative performance.

Details

The primary signature will be evaluated against each permuted dataset in the same manner as for the intact dataset.

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 permuted dataset).

An empirical p-value will be computed based on the percentile rank of the performance of the signature on the intact dataset compared to a null distribution of the performance of the signature on all the permuted datasets.

Value

A result list with the following elements:

Author(s)

Rory Stark

See Also

sigCheck, sigCheckAll, sigCheckRandom, sigCheckKnown

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)
ITERATIONS <- 5 # should be at least 20, 1000 for real checks

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

par(mfrow=c(1,2))
permutedCategories <- sigCheckPermuted(check, toPermute="categories", 
                                       iterations=ITERATIONS)
permutedCategories$checkPval
sigCheckPlot(permutedCategories)
permutedSurvival <- sigCheckPermuted(check, toPermute="survival", 
                                     iterations=ITERATIONS)
permutedSurvival$checkPval
sigCheckPlot(permutedSurvival)

SigCheck documentation built on Nov. 8, 2020, 6:38 p.m.