control_restoration: Restoration metric

In metamaden/rmpipeline: Process DNAm array IDATs into database files

Restoration metric

Description

Single metric, using grn channel

Usage

control_restoration(
  bg.addr,
  rm,
  cname = "Restore",
  gs,
  cdf,
  baseline = 3000,
  biotin.baseline = 1,
  verbose = TRUE
)

Arguments

bg.addr	Probe address of background control probe.
rm	Matrix of control metric signals.
cname	Column name of the control probe.
gs	Green signal data (data.frame, columns are probes, rows are samples, column names are addresses, rownames are samples/GSM IDs).
cdf	Control probe annotations (data.frame, cols = properties, rows = probes).
baseline	Baseline measure for signals (integer, 3000).
biotin.baseline	Baseline to use for biotin controls (integer, 1).
verbose	Whether to show status messages (TRUE).

Value

Control restoration signal.

Examples

cdf <- system.file("extdata", "controldf", "cgcontroldf.rda", 
package = "recountmethylation")

metamaden/rmpipeline documentation built on Jan. 12, 2023, 3:20 p.m.