get_jsontitle: Get sample titles

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

Get sample titles

Description

Mines the sample titles from the instance sample/GSM JSON files. These are included in the mapped metadata tables and used in term mappings.

Usage

get_jsontitle(
  ts,
  json.dname = "gsm_json_filt",
  jsonext.regex = ".*\\.json.filt$",
  json.titlesdf.fn = "gsm_jsontitledf",
  md.dname = "metadata",
  files.dname = "recount-methylation-files"
)

Arguments

ts	Timestamp for the preprocessed metadata table to output (integer or character).
json.dname	Name of directory, in files.dname, containing the instance filtered sample/GSM JSON files ("gsm_json_filt").
jsonext.regex	Regex pattern to identify filtered JSON files (".*\.json.filt$").
json.titlesdf.fn
md.dname	Name of directory, in files.dname, containing the instance metadata files ("metadata).
files.dname	Main recountmethylation instance files directory ("recount-methylation-files").

Value

NULL, produces a file containing the sample titles.

See Also

md_preprocess(); md_postprocess(); get_atables()

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