limmaP: limmaP

In RnBeads: RnBeads

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

Note

Requires limma package

Author(s)

Fabian Mueller

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]])

RnBeads documentation built on March 3, 2021, 2 a.m.