dt_write_rg: Write red and grn signal data to flat tables.

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

Write red and grn signal data to flat tables.

Description

This function takes a filtered list of valid IDAT hlink files and attempts to read their data in chunks with 'minfi::read.metharray()'. To read as many samples as possible, the function attempts to read and combine individual valid samples if an error is thrown for a given chunk or sample subset.

Usage

dt_write_rg(
  probesv,
  hlinkv,
  idatspath,
  reds.path,
  grns.path,
  sepval = " ",
  verbose = TRUE
)

Arguments

probesv	Vector of probe labels.
hlinkv	Vector of GSM IDAT hlink file names, or file basenames.
idatspath	Path to IDAT files directory.
reds.path	Path to new red signal data table.
grns.path	Path to new grn signal data table.
sepval	Separator symbol for data tables.
verbose	Whether to include verbose messages.
min.cols	Minimum data columns to write DNAm data (integer, )

Value

NULL, writes data chunks as side effect

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