RnBiseqSet-class {RnBeads} | R Documentation

## RnBiseqSet Class

### Description

A class for storing the DNA methylation and quality information from bisulfite sequencing experiments

Wrapper function RnBiseqSet

### Usage

    RnBiseqSet(pheno, sites, meth, covg = NULL, assembly = "hg19",
      target = "CpG", summarize.regions = TRUE,
      region.types = rnb.region.types.for.analysis(assembly),
      useff = rnb.getOption("disk.dump.big.matrices"),
      usebigff = rnb.getOption("disk.dump.bigff"), verbose = FALSE)

### Arguments

`pheno` | phenotypic data.
`sites` | CpG site definition, as a `data.frame` with 3 variables: chromosome (of type `character`), position (`integer`) and strand (`character`, one of `"+"`, `"-"` or `"*"`
`meth` | summarized methylation calls as a `matrix` or `ff_matrix`
`covg` | read coverage information as a `matrix` or `ff_matrix`
`assembly` | the genome assembly
`target` | target DNA methylation features (CpG sites)
`summarize.regions` | ...
`region.types` | region annotations for which the methylation data should be summarized
`useff` | flag specifying whether the ff functionality should be used
`usebigff` | flag specifying whether the extended ff functionality should be used (large matrix support for ff)
`verbose` | flag specifying whether the diagnostic messages should be written to the console or to the RnBeads logger, if the latter is initialized

### Details

TBA

### Value

an object of class RnBiseqSet

### Slots

`status`

  Normalization status.

### Methods and Functions

`combine`

  Combines two datasets.

### Author(s)

Pavlo Lutsik

[Package RnBeads version 1.10.8 Index]