dt_makefiles: Make and manage data.table files for red and grn signal

In metamaden/recountmethylation.pipeline: Process DNAm array IDATs into database files

Make and manage data.table files for red and grn signal

Description

Handles options for signal tables, returns paths used to write data chunks.

Usage

dt_makefiles(
  platform = c("hm450k", "epic"),
  hlinkv,
  idatspath,
  destpath,
  version,
  ts,
  overwrite = TRUE,
  fnstem = "compilation",
  sepval = " ",
  verbose = TRUE
)

Arguments

platform	The DNAm array platform of files to read/write (either "hm450k" or "epic").
hlinkv	Vector of GSM IDAT hlinks, or the basenames used to read data.
idatspath	Path to idat files to read
destpath	Destination path to new signal data tables.
version	File version information for file names.
ts	NTP timestamp integer, for filenames (see get_metadata function).
overwrite	Whether to overwrite existing data.table files with same destpath (default TRUE).
fnstem	Filename stem for data tables.
sepval	Separator symbol for tables (" ").
verbose	Whether to return verbose notifications.

Value

list containing dtcond (try conditions results), and new dt paths (reds.path and grns.path)

metamaden/recountmethylation.pipeline documentation built on Dec. 15, 2022, 2:25 a.m.