dtables_rg: Get red and grn signal data tables

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

Get red and grn signal data tables

Description

Generates 2-channel signal data tables. Validates IDATs, handles new paths and data.table options, and provides verbose input from main for loop to write data.

Usage

dtables_rg(
  platform = c("hm450k", "epic"),
  version,
  ts,
  verbose = TRUE,
  gsmint = 60,
  overwrite = TRUE,
  fnstem = "mdat.compilation",
  sepval = " ",
  idatspath = file.path("recount-methylation-files", "idats"),
  destpath = file.path("recount-methylation-files", "compilations")
)

Arguments

platform	The DNAm array platform of files to read/write (either "hm450k" or "epic").
version	Version of the run for data table filenames.
ts	NTP timestamp integer, for filenames (see get_metadata function).
verbose	Whether to return verbose notifications.
gsmint	Number of GSMs to process at a time, typically runs best near 50 samples.
overwrite	Whether to overwrite existing data.table files with same destpath (default TRUE).
fnstem	Filename stem for data tables.
sepval	Separator symbol for data being written (default " ").
idatspath	Path to IDAT files to read.
getnb	Whether to get noob-normalized Beta-vlaues (default: FALSE).

Value

NULL, writes new data tables from IDATs using 'dt_write_rg()'.

Examples

#version = "0.0.1"
#timestamp = get_metadata("title", version)[["timestamp"]]
#dtables_rg(version = version, timestamp = timestamp)

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