make_h5se_gm: Make an H5SE MethySet object from a MethySet HDF5 database...

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

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.

Value

NULL, generates a new h5se file.

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