make_h5_gm: Make an HDF5 db file with MethylSet data, from an...
In metamaden/rmpipeline: Process DNAm array IDATs into database files

make_h5_gm

R Documentation

Make an HDF5 db file with MethylSet data, from an RGChannelSet h5se file

Description

Makes an HDF5 db file with raw/unnormalized methylated and unmethylated signal, including rows and columns as datasets.

Usage

make_h5_gm(
  dbn,
  version,
  ts,
  blocksize = 65,
  files.dname = "recount-methylation-files",
  comp.dname = "compilations",
  platform = c("hm450k", "epic"),
  newfnstem = "remethdb",
  verbose = TRUE,
  dsv = c("meth", "unmeth"),
  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
`platform`	Array platform (either "hm450k" or "epic").
`newfnstem`	New filename stem for h5 file.
`verbose`	Whether to return verbose messages (default TRUE).
`dsv`	Vector of new datasets to add to h5 HDF5 database.
`replace.opt`	Whether to replace h5 files with duplicate filename (default TRUE).