md_agg: Aggregate available metadata tables
In metamaden/rmpipeline: Process DNAm array IDATs into database files

md_agg

R Documentation

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).