intensities.by.color {RnBeads} | R Documentation

## intensities.by.color

### Description

Rearranges information from "M" and "U" slots of a RnBeadsRawSet object by color channel.

### Usage

    intensities.by.color(
      raw.set,
      address.rownames = TRUE,
      add.oob = all(!is.null(M0(raw.set)), !is.null(U0(raw.set))),
      add.controls = !is.null(qc(raw.set)),
      add.missing = TRUE,
      re.separate = FALSE
    )

### Arguments

`raw.set` | Methylation dataset as an instance of `RnBeadRawSet` object.
`address.rownames` | if `TRUE` the rows of the returned matrices are named with the with the corresponding Illumina probe addresses
`add.oob` | if `TRUE` the "out-of-band" intensities are included
`add.controls` | if `TRUE` the control probe intensities are included
`add.missing` | if `TRUE` the rows for the probes missing in `raw.set` is imputed with `NA` values
`re.separate` | if `TRUE` the type I and type II intensities, as well as the out-of-band and control probe intensities (if set to `TRUE`), will be returned as separate elements per channel and not as concatenated rows.

### Value

A `list` with elements `Cy3` and `Cy5` containing average bead intensities measured for each each probe in the green and red channels, respectively. Exception, if `re.separate` is `TRUE` a `list` with elements `Cy3.I`, `Cy5.I`, and `II` will be returned. The elements `Cy3.I.oob`, `Cy5.I.oob` and also `Cy3.ctl`, `Cy5.ctl` will be returned if the respective parameters (`add.oob` and `add.ctl`) are set to true.

### Author(s)

Pavlo Lutsik, Nathan Steenbuck

[Package RnBeads version 2.12.2 Index]