control_specificity: Specificity metrics

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

Specificity metrics

Description

Three metrics (two for I and one for type II), for each color channel and BeadArray probe type.

Usage

control_specificity(
  rm,
  rs,
  gs,
  cdf,
  baseline = 3000,
  cnames = c("Specificity_I_red", "Specificity_I_grn", "Specificity_II"),
  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 specificity metrics.

Examples

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

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