evaluateGeneSetUncertainty: Quantify gene set uncertainty

In GiANT: Gene Set Uncertainty in Enrichment Analysis

Description

A robustness measure that quantifies the uncertainty of a gene set by performing a resampling experiment and can be used in the robustness parameter of gsAnalysis.

Usage

evaluateGeneSetUncertainty(
	...,
	dat,
	geneSet,
	analysis,
	numSamplesUncertainty,
	blockSize = 1,
	k = seq(0.01, 0.99, by=0.01),
	signLevel = 0.05,
	preprocessGeneSet = FALSE,
	cluster = NULL)

Arguments

...	Additional parameters for the different steps of the analysis pipeline, depending on the concrete configuration supplied in analysis.
dat	A numeric matrix of gene expression values for all analyzed genes. Here, each row corresponds to one gene, and each column corresponds to one sample. The rows must be named with the gene names used in the gene sets.
geneSet	A vector containing the names of genes in a gene set. All genes set must correspond to the row names of dat.
analysis	The parameters of the analysis that is applied to the perturbed copies of the gene set. These parameters are described by an object of class gsAnalysis as returned by the function gsAnalysis or the predefined analysis descriptors in predefinedAnalyses.
numSamplesUncertainty	The number of resampling experiments which should be applied to estimate the robustness of geneSet.
blockSize	Number of genes in one resampled block.
k	A vector of percentages of genes in the randomized gene sets that should be taken from the original gene set. The remaining genes are chosen randomly. For each value a resampling experiment is performed.
signLevel	The significance level for the significance assessment of the gene sets (defaults to 0.05).
preprocessGeneSet	Specifies whether the gene sets in geneSets should be preprocessed or not. If set to TRUE, all genes that are not part of the data set (i.e. not in rownames(dat)) are removed from the gene sets.
cluster	If the analyses should be applied in parallel for the different values of k, this parameter must hold an initialized cluster as returned by makeCluster. If this parameter is NULL, the analyses are performed sequentially.

Details

The uncertainty analysis repeatedly replaces parts of the original gene sets by random genes and calculating the gene set statistics for these randomized gene sets. This yields a distribution of gene set statistic values for slightly modified variants of the original gene set.

Value

Returns a list (of class uncertaintyResult) with the following elements:

• uncertainty The calculated stability of the original gene set.

• confidenceValues A matrix of quantiles of gssValues (signLevel, 0.5, 1-signLevel). One row for each value in k.

• uncertaintyEvaluations A list with one entry per value in k containing the following elements:

  • confidenceValues Quantiles of gssValues: signLevel, 0.5, 1-signLevel.

  • gssValues A vector of gene set statistic values, one for each randomly sampled gene set.

  • uncertainGeneSets A matrix containing all partially random gene sets.

  • k The percentage of genes in the randomized gene sets taken from the original gene set.

• signLevel The significance level used for this analysis.

• originalGeneSetValues Result of geneSetAnalysis for the original geneSet.

See Also

geneSetAnalysis, gsAnalysis, gls, transformation, gss, plot.uncertaintyResult

Examples

# load data
require(GlobalAncova)
data(vantVeer)
data(phenodata)
data(pathways)

res <- evaluateGeneSetUncertainty(
	# parameters for evaluateGeneSetUncertainty
	dat = vantVeer,
	geneSet = pathways[[1]],
	analysis = analysis.averageCorrelation(),
	numSamplesUncertainty = 10,
	k = seq(0.1,0.9, by=0.1),
	# additional parameters for analysis.averageCorrelation
	labs = phenodata$metastases,
	numSamples = 10)

GiANT documentation built on Oct. 23, 2020, 7:56 p.m.