make_h5se_gr: Make an h5se object from an h5se gr file

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

Make an h5se object from an h5se gr file

Description

Make an h5se object from an h5se gr file

Usage

make_h5se_gr(
  version,
  ts,
  dbn,
  files.dname = "recount-methylation-files",
  comp.dname = "compilations",
  platform = c("hm450k", "epic"),
  replaceopt = TRUE,
  verbose = TRUE,
  add.metadata = FALSE,
  pdata = NULL,
  newdnstem = "remethdb",
  semd = list(title = paste0("GenomicMethylSet HDF5-", "SummarizedExperiment"),
    preprocessing = paste0("Normalization with", " out-of-band ", "signal (noob)"))
)

Arguments

version	Version for new filenames.
ts	NTP timestamp.
dbn	Path to HDF5 database file to read data from.
files.dname	Files dir name for instance ("recount-methylation-files")
comp.dname	Compilations dir name, located in files.dname
replaceopt	Whether to overwrite existing file of same name as new file (default = TRUE).
verbose	Whether to return verbose messages (default TRUE).
add.metadata	Whether to add samples metadata (boolean, FALSE).
pdata	Samples metadata as a DataFrame, path to file, or NULL.
newdnstem	Character stme for new h5se object file ("remethdb_h5se-gr").

Value

NULL, generates a new h5se file.

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