mval,RnBSet-method {RnBeads} | R Documentation

## mval-methods

### Description

Extracts DNA methylation information (M values) for a specified set of genomic features.

### Usage

    ## S4 method for signature 'RnBSet'
    mval(object, type = "sites", row.names = FALSE,
      epsilon = 0)

### Arguments

`object` | dataset of interest.
`type` | `character` singleton. If this is set to `"sites"` (default), DNA methylation information for each available site is returned. Otherwise, this should be one of region types for for which summarized DNA methylation information is computed in the given dataset.
`row.names` | Flag indicating of row names are to be generated in the result.
`epsilon` | Threshold of beta values to use when adjusting for potential M values close to +infinity or -infinity. See `rnb.beta2mval` for more details.

### Value

`matrix` with methylation M values.

### See Also

`meth` for extracting methylation beta values

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    ## per-site M-value matrix
    mm<-mval(rnb.set.example, row.names=TRUE)
    head(mm)
    ## M-values for each covered gene
    gmm<-mval(rnb.set.example, type="gene", row.names=TRUE)
    head(gmm)

[Package RnBeads version 1.12.1 Index]