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

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