Correlation between aberrant exon usage and expression levels for a number of gene sets.

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Description

The function makes use of the corAndPValue function from the WGCNA package to calculate the Pearson correlation between sample-wise aberrant exon usage amounts and expression levels of all genes for all gene sets defined by the input parameter list geneSets.

Usage

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    geneSetCorrelation(geneSets, geneAnnotation, geneSummaries, tra, 
        noGeneSets)

Arguments

geneSets

A data.frame with a number of gene lists to be included in the correlation analysis. An example data.frame of 1,454 lists of genes (specified by Affymetrix transcript cluster id's and gene symbols) is included in the package, and will be accessible by issuing the command 'data(genesets)'. The example data.frame contains a complete collection of all Gene Ontology gene sets included in the Molecular Signatures Database v3.1.

geneAnnotation

A data.frame with Affymetrix transcript cluster id's and gene symbols for all 22,011 genes included in the Affymetrix 'core' set.

geneSummaries

A data.frame with gene-level expression values for all samples, returned from the 'readGeneSummaries' function.

tra

List with total relative amounts of aberrant exon usage for all samples obtained using the 'aberrantExonUsage' function.

noGeneSets

Optional argument specifying how many gene sets to include in the analysis.

Value

A data.frame with one row for each data set used as input, and columns for name of set, number of genes, number of significant positively/negatively correlated genes in the set, and median correlation strength.

Examples

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# Load data
    data(geneSets)
    data(geneAnnotation)
    fs <- firmaAnalysis(useToyData=TRUE)
    gs <- readGeneSummaries(useToyData=TRUE)
    tra <- aberrantExonUsage(1.0, fs)
# Calculate correlation in other gene sets
    crs <- geneSetCorrelation(geneSets, geneAnnotation, gs, tra, 50)