sampling {globaltest}R Documentation

Sampling random 'pathways' for the Global Test

Description

For every pathway in a result of globaltest, calculates how many randomly drawn groups of genes of the same size have a smaller or equal p-value.

Usage

sampling(gt, geneset, ndraws = 10^3)

Arguments

gt The output of a call to globaltest.
geneset The name or number of the geneset(s) to be used (only necessary if multiple genesets were tested).
ndraws The number of random pathways to be used.

Details

For every pathway in gt[geneset], a number ndraws random 'pathways' is selected by randomly sampling sets of genes of the same size as the tested pathway. A 'comparative p-value' is calculated by counting what proportion of the random pathways has a larger standardized test statistic (Q - EQ) / sd(Q) than the tested pathway.

Value

An object of class gt.result.

Note

The function sampling cannot be applied to a gt.result object resulting from a call to permutations.

Author(s)

Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting

References

Jelle J. Goeman, Jan Oosting, Anne-Marie Cleton-Jansen, Jakob, K. Anninga, Hans C. van Houwelingen (2005) Testing association of a pathway with survival. Bioinformatics 21, 1950-1957. See also the vignette Globaltest.pdf that comes with this package.

See Also

globaltest, permutations, sampleplot, geneplot.

Examples

    # Breast cancer data (ExpressionSet) from the Netherlands Cancer
    # Institute with annotation:
    data(vandeVijver)
    data(annotation.vandeVijver)

    gt <- globaltest(vandeVijver, "StGallen", annotation.vandeVijver)

    sampling(gt, ndraws=100)

[Package globaltest version 4.12.0 Index]