control_nonpolymorphic: Non-polymorphic metric

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

Non-polymorphic metric

Description

Two metrics, one per color channel.

Usage

control_nonpolymorphic(
  rm,
  rs,
  gs,
  cdf,
  baseline = 3000,
  cnames = c("Non-polymorphic_red", "Non-polymorphic_green"),
  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).
baseline	Baseline measure for signals (integer, 3000).
cnames	Vector of control probe column names for the metric.
biotin.baseline	Baseline to use for biotin controls (integer, 1).
verbose	Whether to show status messages (TRUE).

Value

Control non-polymorphic metrics.

Examples

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

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