BiSeq (version 1.12.0)

globalTest: Test whether at least one CpG is differentially methylated in a given genomic region

Description

This method is a wrapper for conveniently invoking the globaltest method gt on a BSrel-class object. The globaltest can be applied to test against a high dimensional alternative in various regression models. E.g., it can be used to test whether at least one CpG is differentially methylated between two groups.

Usage

globalTest(response, alternative, ...)

Arguments

response

The response vector of the regression model. May be supplied as a vector or as a formula object. In the latter case, the right hand side of response defines the null hypothesis. The default null hypopthesis is ~1, i.e. only an intercept.

alternative

An object of BSrel-class defining the alternative. The CpGs are used as explanatory variable in the alternative regression model. The null hypothesis is that the coefficients of all CpGs are zero. If response is given as formula, colData(alternative) is used to obtain the respective data.

...

Other arguments passed to the gt method. The argument subsets can be given as GRanges-class object. Then, the globaltest is applied for each region using only the CpGs lying within the respective region. This is useful for, e.g., testing all promoter regions within function call.

Value

The function returns an object of class gt.object. Several operations and diagnostic plots for this class are provided by the globaltest package.

Details

For details see the documentation of the gt method in package globaltest.

References

Goeman, J. J., van de Geer, S. A., and van Houwelingen, J. C. (2006). Testing against a high-dimensional alternative. Journal of the Royal Statistical Society Series B- Statistical Methodology, 68(3):477-493.

See Also

link{gt}, link{BSrel}

Examples

data(rrbs)
rrbs <- rawToRel(rrbs)
regions <- GRanges(IRanges(start=c(850000, 1920000, 500), end=c(879000, 1980000, 600)),
                   seqnames=c("chr1", "chr2", "chr3"))

globalTest(group~1, rrbs)
globalTest(group~1, rrbs, subsets=regions)