make_h5_gr: Make an HDF5 h5 file with GenomicRatioSet data, from an...

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

Make an HDF5 h5 file with GenomicRatioSet data, from an RGChannelSet h5se file

Description

Makes an HDF5 h5 file containing noob-normalized Beta-values, including rows and columns as separate datasets.

Usage

make_h5_gr(
  dbn,
  version,
  ts,
  blocksize = 65,
  files.dname = "recount-methylation-files",
  comp.dname = "compilations",
  verbose = TRUE,
  platform = c("hm450k", "epic"),
  newfnstem = "remethdb",
  replace.opt = TRUE
)

Arguments

dbn	Path to the RGChannelSet H5SE data directory.
version	Version for new h5 file.
ts	Timestamp for new h5 file.
blocksize	Size of blocks/number of samples to process at a time (default 65).
files.dname	Files dir name for instance ("recount-methylation-files")
comp.dname	Compilations dir name, located in files.dname
verbose	Whether to return verbose messages (default TRUE).
platform	Array platform (either "hm450k" or "epic").
newfnstem	New filename stem for h5 file.
replace.opt	Whether to replace h5 files with duplicate filename (default TRUE).

Value

Path to new h5 object.

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