make_h5se_gm: Make an H5SE MethySet object from a MethySet HDF5 database...
In metamaden/rmpipeline: Process DNAm array IDATs into database files

make_h5se_gm

R Documentation

Make an H5SE MethySet object from a MethySet HDF5 database file

Description

Make an H5SE MethySet object from a MethySet HDF5 database file

Usage

make_h5se_gm(
  dbn,
  version,
  ts,
  platform = c("hm450k", "epic"),
  files.dname = "recount-methylation-files",
  comp.dname = "compilations",
  replaceopt = TRUE,
  verbose = TRUE,
  add.metadata = FALSE,
  pdata = NULL,
  newdnstem = "remethdb",
  semd = list(title = paste0("GenomicMethylSet HDF5-", "SummarizedExperiment"),
    preprocessing = "raw")
)

Arguments

`dbn`	Name of the h5 file to read data from.
`version`	Version for new filenames.
`ts`	NTP timestamp.
`platform`	Array platform (either "hm450k" or "epic").
`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`	Metadata object obtained from pData(se).
`newdnstem`	Stem for new h5se object file.