control_bsconversion: Bisulfite conversion I and II

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

Bisulfite conversion I and II

Description

Three metrics. For Bisulfite conversion I, calculates one metric from controls C1-3 vs. U1-3 in green channel, the other from controls C4-6 vs. U4-6 in red channel. For Bisulfite conversion II, calculates one metric.

Usage

control_bsconversion(
  rm,
  rs,
  gs,
  cdf,
  baseline = 3000,
  cnames = c("Bisulfite_conversion_I_red", "Bisulfite_conversion_I_green",
    "Bisulfite_conversion_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 bisulfite conversion metrics.

Examples

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

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