append_md: Append metadata to DNAm data compilations

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

Append metadata to DNAm data compilations

Description

Append metadata to DNAm data compilations. Handles metadata addition for either HDF5 or HDF5-SummarizedExperiment compilation files.

Usage

append_md(
  ts,
  files.dname = "recount-methylation-files",
  md.dname = "metadata",
  comp.dname = "compilations",
  comp.fnv = c(".*_h5_.*", ".*_h5se_.*"),
  mdall.fnstr = "mdall_*",
  verbose = TRUE
)

Arguments

ts	Timestamp.
files.dname	Files dir name for the instance ("recount-methylation-files")
md.dname	Metadata dir name for the instance ("metadata"), contained in files.dname.
comp.dname	Compilations dir name for instance ("compilations"), contained in files.dname.
comp.fnv	Vector of regular expression patterns to filter compilation files list.
mdall.fnstr	Filename string stem to detect aggregate metadata table at md.dname.
verbose	Whether to show status messages (TRUE).

Value

NULL, if all appends successful, otherwise a list of the compilation files for which appends weren't successful.

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