covg,RnBSet-method {RnBeads} | R Documentation

## covg-methods

### Description

Extract coverage information from an object of `RnBSet` class.

### Usage

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

### Arguments

`object` | Dataset of interest.
`type` | `character` singleton. If `sites` DNA methylation information per each available site is returned. Otherwise should be one of region types for for which the summarized coverage information is available
`row.names` | Flag indicating of 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

coverage information available for the dataset in the form of a `matrix`.

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    ## per-site beta-value matrix
    cvg<-covg(rnb.set.example, row.names=TRUE)
    head(cvg)

[Package RnBeads version 1.12.1 Index]