RnBeads (version 1.4.0)

limmaP: limmaP

Description

applies hierarchical modeling anlalogous to differential expression employed in the limma package and returns p-values for differential methylation

Usage

limmaP(X, inds.g1, inds.g2 = -inds.g1, adjustment.table = NULL, fun.conversion = rnb.beta2mval, paired = FALSE)

Arguments

X

Matrix on which the test is performed for every row

inds.g1

column indices of group 1 members

inds.g2

column indices of group 2 members

adjustment.table

a data.frame containing variables to adjust for in the testing

fun.conversion

conversion function to transform the beta values into M values. By default, it is the logit function with adjustment for infinity values. See rnb.beta2mval for details.

paired

should a paired analysis model be used. If so, the first index in inds.g1 must correspond to the first index in inds.g2 and so on.

Value

vector of p-values resulting from limma's differential analysis

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
meth.mat <- meth(rnb.set.example)
sample.groups <- rnb.sample.groups(rnb.set.example)[[1]]
p.vals <- limmaP(meth.mat,sample.groups[[1]],sample.groups[[2]])