limmaP {RnBeads} | R Documentation

## 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

### 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]])

[Package RnBeads version 1.12.1 Index]