get_qcmetrics: Get quality metrics from DNAm assays

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

Get quality metrics from DNAm assays

Description

Calculates quality metrics from DNAm assays contained in the compilation files. These include signals for 17 BeadArray controls, 2 controls for the methylated and unmethylated signals, and predicted genotypes by sample using methods in the ewastools package.

Usage

get_qcmetrics(
  ts,
  rgset.fname,
  gmset.fname,
  mdqc.fname = "mdqc",
  athresh = 0.1,
  nsamp.block = 50,
  md.dname = "metadata",
  comp.dname = "compilations",
  files.dname = "recount-methylation-files",
  verbose = TRUE
)

Arguments

ts	Timestamp for the preprocessed metadata table to output (integer or character).
mdqc.fname	Name of the quality metrics table output ("mdqc")
athresh	Similarity threshold (percent similarity) for the ewastools predicted genotype (decimal, 0.1).
nsamp.block	Samples per data block processed (integer, 50).
md.dname	Name of directory, in files.dname, containing the instance metadata files ("metadata).
files.dname	Main recountmethylation instance files directory ("recount-methylation-files").
verbose	Whether to show status messages (TRUE).

Value

NULL, produces a table of quality metrics.

See Also

md_predictions(); md_preprocess(); md_postprocess()

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