control_targetremoval: Target removal metrics

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

Target removal metrics

Description

Two metrics, one for each BeadArray probe type, each calculated from green color channel signals.

Usage

control_targetremoval(
  rm,
  rs,
  gs,
  cdf,
  verbose = TRUE,
  cnames = c("Target_removal_1", "Target_removal_2"),
  baseline = 3000,
  biotin.baseline = 1
)

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).
verbose	Whether to show status messages (TRUE).
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).

Value

Control target removal metrics.

Examples

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

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