RnBeadRawSet-class {RnBeads} | R Documentation

## RnBeadRawSet-class

### Description

Main class for storing HumanMethylation micorarray data which includes intensity information

### Usage

    RnBeadRawSet(
      pheno,
      probes,
      M,
      U,
      M0 = NULL,
      U0 = NULL,
      bead.counts.M = NULL,
      bead.counts.U = NULL,
      p.values = NULL,
      qc = NULL,
      platform = "450k",
      beta.offset = 100,
      summarize.bead.counts = TRUE,
      summarize.regions = TRUE,
      region.types = rnb.region.types.for.analysis(ifelse(platform == "MMBC", "mm10",
        "hg19")),
      useff = rnb.getOption("disk.dump.big.matrices"),
      ffcleanup = FALSE
    )

### Arguments

`pheno` | Phenotypic data.
`probes` | `character` vector of Infinium(R) probe identifiers
`M` | Matrix of intensities for the probes measuring the abundance of methylated molecules
`U` | Matrix of intensities for the probes measuring the abundance of unmethylated molecules
`M0` | Matrix of "out-of-band" intensities for the probes measuring the abundance of methylated molecules
`U0` | Matrix of "out-of-band" intensities for the probes measuring the abundance of unmethylated molecules
`bead.counts.M` | Matrix of bead counts per probe.
`bead.counts.U` | Matrix of bead counts per probe.
`p.values` | Matrix of detection p-values.
`qc` | ...
`platform` | `character` singleton specifying the microarray platform: `"450k"` corresponds to HumanMethylation450 microarray, and `"27k"` stands for HumanMethylation27.
`beta.offset` | A regularization constant which is added to the denominator at beta-value calculation
`summarize.bead.counts` | If `TRUE` the coverage slot is filled by summarizing the `bead.counts.M` and `bead.counts.U` matrices. For type I probes the summarization is done using `min` operation, while for type II probes the bead counts should be identical in both supplied matrices
`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
`ffcleanup` | If `TRUE` and disk dumping has been enabled the data of the input `ff` objects will be deleted

### Value

an object of class RnBeadRawSet

### Slots

`pheno`

  Phenotypic data.

`M`

  `matrix` of intensities for the probes measuring the abundance of methylated molecules.

`U`

  `matrix` of intensities for the probes measuring the abundance of unmethylated molecules.

`M0`

  `matrix` of "out-of-band" intensities for the probes measuring the abundance of methylated molecules.

`U0`

  `matrix` of "out-of-band" intensities for the probes measuring the abundance of unmethylated molecules.

`bead.counts.M`

  `matrix` of bead counts per probe.

`bead.counts.U`

  `matrix` of bead counts per probe.

### Methods and Functions

`samples`

  Gets the identifiers of all samples in the dataset.

`M`

  Get the matrix of intensities for the probes measuring the abundance of methylated molecules.

`U`

  Get the matrix of intensities for the probes measuring the abundance of unmethylated molecules.

`intensities.by.color`

  Get probe intensities in each color channel.

### Author(s)

Pavlo Lutsik

[Package RnBeads version 2.12.2 Index]