meth,RnBSet-method {RnBeads} | R Documentation

## meth-methods

### Description

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

### Usage

    ## S4 method for signature 'RnBSet'
    meth(object, type = "sites", row.names = FALSE,
      i = NULL, j = NULL)

### 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 if row names are to be generated in the result.
`i` | indices of sites/regions to be retrieved. By default (`NULL`), all will be retrieved.
`j` | indices of samples to be retrieved. By default (`NULL`), all will be retrieved.

### Value

`matrix` with methylation beta values.

### See Also

`mval` for calculating M values

### Examples

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

[Package RnBeads version 2.0.1 Index]