get_atables: Generate study annotation tables

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

Generate study annotation tables

Description

Generate a list of study annotation tables from filtered sample JSON files. Sample/GSM JSON files should be filtered to remove study-level information, retaining just sample-level metadata.

Usage

get_atables(
  ts,
  atable.fn = "geo_gse-atables_list",
  eq.dname = "equery",
  md.dname = "metadata",
  json.filt.dname = "gsm_json_filt",
  files.dname = "recount-methylation-files",
  verbose = TRUE
)

Arguments

ts	Timestamp for the preprocessed metadata table to output (integer or character).
atable.fn	Name of the annotation tables file to output ("geo_gse-atables_list)
eq.dname	Name of directory, in files.dname, containing the equery files produced by the server ("equery").
md.dname	Name of directory, in files.dname, containing the instance metadata files ("metadata).
json.filt.dname	Name of directory, in files.dname, containing the filtered GSM JSON files (e.g. containing only sample metadata, "gsm_json_filt")
files.dname	Main recountmethylation instance files directory ("recount-methylation-files").
verbose	Whether to show status messages (TRUE).

Value

NULL, produces the tables list file.

See Also

md_preprocess(); md_postprocess()

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