globalTest {BiSeq} | R Documentation |
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.
globalTest(response, alternative, ...)
response |
The response vector of the regression model. May be
supplied as a vector or as a |
alternative |
An object of |
... |
Other arguments passed to the |
For details see the documentation of the gt
method in
package globaltest.
The function returns an object of class gt.object
. Several
operations and diagnostic plots for this class are provided by the
globaltest package.
Hans-Ulrich Klein
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.
link{gt}
, link{BSrel}
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)