md_agg: Aggregate available metadata tables

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

Aggregate available metadata tables

Description

Detects valid metadata at md.dpath, then aggregates these into a single composite table.

Usage

md_agg(
  ts = NULL,
  platform = NULL,
  lfn = NULL,
  id.cname = "gsm",
  mda.fn = "mdall",
  md.fnv = c("^md_postprocess.*", "^mdmod_dnam-predictions_.*", "^mdqc_.*",
    "^mdrep_.*", "^md_msrapout_.*", "gsm_jsontitledf_.*"),
  md.dpath = file.path("recount-methylation-files", "metadata"),
  verbose = TRUE
)

Arguments

ts	Timestamp.
platform	The DNAm array platform used.
lfn	Optional list of filenames. If NULL, automatically detect valid metadata files (NULL).
id.cname	Column name for sample IDs, which should be present in each table to be compiled ("gsm").
mda.fn	Filename stem of new aggregate metadata table to save ("mdall").
md.fnv	Vector of regex patterns to detect valid metadata tables.
md.dpath	Path to metadata directory.
verbose	Whether to show status messages (TRUE).

Value

NULL, stores aggregate/composite metadata table.

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