intensities.by.color: intensities.by.color

In RnBeads: RnBeads

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

RnBeads documentation built on March 3, 2021, 2 a.m.