get_gsm_exclude: Get GSM IDs to exclude for this instance

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

Get GSM IDs to exclude for this instance

Description

Get the GSM IDs to exclude from target/download for this instance. The IDs vector informs an updated edirect query filter object (e.g. file named "gsequery_filt.*").

Usage

get_gsm_exclude(
  md = NULL,
  se.path = NULL,
  fn.str = "gsm_exclude",
  fn.dpath = ".",
  id.gsm.cname = "gsm",
  verbose = TRUE
)

Arguments

md	Metadata table containing sample ID column (id.gsm.cname, e.g. "gsm"). If this is NULL, try loading an se object instead.
se.path	Path to a valid HDF5-SummarizedExperiment to check/load.
fn.str	Name of sample IDs vector file to save.
fn.dpath	Directory path to save samples ID vector.
id.gsm.cname	Name of column containing the GSM IDs.
verbose	Whether to show verbose status messages.

Value

Vector of GSM IDs, with option to save.

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