intensities.by.color {RnBeads} | R Documentation

## intensities.by.color

### Description

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

### 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)

### 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 correspoding 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

### Value

a `list` with elements `Cy3` and `Cy5` containing average bead intensities measured for each each probe in the green and red channels, respectively.

### Author(s)

Pavlo Lutsik

[Package RnBeads version 2.2.0 Index]