md_preprocess: Preprocess sample metadata

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

Preprocess sample metadata

Description

Preprocess sample metadata by coercing JSON-formatted metadata files into a flat matrix, with regex pattern matching to identify and categorize various variable types. Additional data such as the sample titles contained in the file declared by the titles.fn argument.

Usage

md_preprocess(
  ts,
  mdpre.fn = "md_preprocess",
  md.dname = "metadata",
  titlesfn.str = "gsm_jsontitledf",
  atablefn.str = "geo_gse-atables_list",
  files.dname = "recount-methylation-files",
  verbose = TRUE
)

Arguments

ts	Timestamp for the preprocessed metadata table to output (integer or character).
mdpre.fn	Name of preprocessed metadata table file to output ("md_preprocess").
md.dname	Name of directory, in files.dname, containing the instance metadata files ("metadata).
titlesfn.str	Name of sample/GSM titles file ("gsm_jsontitledf).
atablefn.str	Name of study annotation tables file ("geo_gse-atables_list")
files.dname	Main recountmethylation instance files directory ("recount-methylation-files").
verbose	Whether to show status messages (TRUE).

Value

NULL, produces the mdpre preprocessed metadata table.

See Also

md_postprocess()

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