control_biotinstaining: Biotin staining metrics

In metamaden/recountmethylation.pipeline: Process DNAm array IDATs into database files

Biotin staining metrics

Description

Two metrics, 1 per color channel

Usage

control_biotinstaining(
  rm,
  rs,
  gs,
  cdf,
  cnames = c("Biotin_red", "Biotin_green"),
  baseline = 3000,
  biotin.baseline = 1,
  verbose = TRUE
)

Arguments

rm	Matrix of control metric signals.
rs	Red signal data (data.frame, columns are probes, rows are samples, column names are addresses, rownames are samples/GSM IDs).
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).
cnames	Vector of control probe column names for the metric.
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 biotin staining signal.

Examples

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

metamaden/recountmethylation.pipeline documentation built on Dec. 15, 2022, 2:25 a.m.