RnBeadSet-class {RnBeads} | R Documentation

## RnBeadSet Class

### Description

Stores the preprocessed information from HumanMethylation experiments

### Usage

    RnBeadSet(
      pheno,
      probes,
      betas,
      p.values = NULL,
      bead.counts = NULL,
      qc = NULL,
      platform = "450k",
      summarize.regions = TRUE,
      region.types = rnb.region.types.for.analysis(ifelse(platform == "MMBC", "mm10",
        "hg19")),
      useff = rnb.getOption("disk.dump.big.matrices")
    )

### Arguments

`pheno` | Phenotypic data.
`probes` | `character` vector of Infinium(R) probe identifiers
`betas` | `matrix` or `ff_matrix` of beta values. If `probes` are missing should contain Infinium probe identifiers as row names.
`p.values` | `matrix` or `ff_matrix` of detection p-values.
`bead.counts` | ...
`qc` | ...
`platform` | `character` singleton specifying the microarray platform: `"450k"` corresponds to HumanMethylation450 microarray, and `"27k"` stands for HumanMethylation27.
`summarize.regions` | ...
`region.types` | A `character` vector specifying the region types, for which the methylation infromation will be summarized.
`useff` | If `TRUE` the data matrices will be stored as `ff` objects

### Details

There are multiple ways to create an object of type `RnBeadSet`:

Loading from files

  Dataset can be loaded from text or binary files. See the function `rnb.execute.import` for more details.

Downloading from GEO

  See the function `rnb.read.geo` for details.

Converting from `MethyLumiSet`

  ...

### Value

an object of class RnBeadSet

### Slots

`pval.sites`

  `matrix` of detection p-values with the same dimensions as `betas`, or `NULL` if the detection p-values are not available.

`pval.regions`

  `list` of methylation `matrix` objects, one per available region type. Every row in a matrix corresponds to a methylation site, and every column - to a sample.

`covg.sites`

  `matrix` of bead counts per probe with the same dimensions as `betas`, or `NULL` if this data are not available.

`qc`

  Quality control probe information in the form of a `list` of two elements - `"Cy3"` and `"Cy5"`, storing intensities of probes on the green and red channels, respectively. This slot's value is `NULL` if no control probe information is available.

### Methods and Functions

`samples`

  Gets the identifiers of all samples in the dataset.

`pheno`

  Gets the phenotypic and processing data of the dataset.

`meth`

  Gets the `matrix` of methylation beta-values of the dataset.

`dpval`

  Gets the `matrix` of detection p-values of the dataset.

`covg`

  Gets the `matrix` of bead counts of the dataset.

`qc`

  Gets the intensities of the quality control probes.

`remove.sites`

  Removes probes from the dataset.

`remove.samples`

  Removes samples from the dataset.

`combine`

  Combines two datasets.

### Author(s)

Pavlo Lutsik

[Package RnBeads version 2.12.2 Index]