control_hybridization: Hybridization metrics

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

Hybridization metrics

Description

Two metrics, one comparing high vs. medium level, the other comparing medium vs. low level. Both metrics calculated from Green color channel signals.

Usage

control_hybridization(
  rm,
  rs,
  gs,
  cdf,
  baseline = 3000,
  cnames = c("Hybridization_medium-vs-high", "Hybridization_low-vs-medium"),
  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 hybridization metrics.

Examples

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

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