get_msrap: Get the pipeline data files as a flat table

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

Get the pipeline data files as a flat table

Description

Reads data in the sample/GSM-level metadata files produced by the pipeline and "map_msrap.py" script. Data is read and stored as a flat table ready to be appended to other metadata for the instance.

Usage

get_msrap(
  ts = NULL,
  files.dir = "recount-methylation-files",
  md.dname = "metadata",
  msrap.dname = "gsm_msrap_outfiles",
  msrap.regex.str = "^msrapout.*",
  gsmid.fnindex = 2,
  gmap.fn = "md_msrapout"
)

Arguments

ts	NTP timestamp for the new metadata table (string, NULL).
files.dir	Files dir for the instance ("recount-methylation-files").
md.dname	Metadata dir name, located in the files.dir ("metadata").
msrap.dname	Name of dir, located in the files.dir, containing pipeline outputs for samples/GSM IDs ("gsm_msrap_outfiles").
msrap.regex.str	Regex pattern string for valid metadata pipeline output files ("^msrapout.*").
gsmid.fnindex	File name index of the GSM ID for valid metadata pipeline output files (2).
gmap.fn	File name stem of the new mapped metadata table ("md_msrapout").

Value

NULL, outputs the mapped data table to the metadata directory.

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