make_h5se_rg: make_h5se_rg
In metamaden/rmpipeline: Process DNAm array IDATs into database files

make_h5se_rg

R Documentation

make_h5se_rg

Description

Make an RGChannelSet HDF5-SummarizedExperiment object from an HDF5 database.

Usage

make_h5se_rg(
  platform = c("hm450k", "epic"),
  files.dname = "recount-methylation-files",
  comp.dname = "compilations",
  version = "0.0.1",
  ts = "1590090412",
  dbn = "remethdb_1590090412_0-0-1.h5",
  newfnstem = "remethdb_h5se-rg",
  dsnv = c("redsignal", "greensignal"),
  add.metadata = FALSE,
  mdpath = NULL,
  dsn.md = "mdpost",
  dsn.md.cn = paste0(dsn.md, ".colnames"),
  verbose = TRUE,
  replace.opt = TRUE,
  dsn.rnv = c(paste0(dsnv[1], ".rownames"), paste0(dsnv[2], ".rownames")),
  dsn.cnv = c(paste0(dsnv[1], ".colnames"), paste0(dsnv[2], ".colnames")),
  semd = list(title = paste0("RGChannelSet HDF5-", "SummarizedExperiment"),
    preprocessing = "raw")
)

Arguments

`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 ("compilations").
`version`	The data file version.
`ts`	Data file NTP timestamp (character).
`dbn`	Name/path of HDF5 database file.
`newfnstem`	File name stem for new database file.
`dsnv`	Table names vector.
`add.metadata`	Whether to add samples metadata (boolean, FALSE).
`mdpath`	Path to metadata pile (if NULL, search the HDF5 database).
`dsn.md`	Metadata table name, used if add.metadata is TRUE.
`dsn.md.cn`	Metadata columns object, used if add.metadata is TRUE.
`verbose`	Whether to show status messages (boolean, TRUE).
`replace.opt`	Whether to replace/overwrite old H5SE object (TRUE).
`dsn.rnv`	Names vector of rownames objects in HDF5 database.
`dsn.cnv`	Names vector of colnames objects in HDF5 database.
`semd`	Metadata vector for new H5SE object to be written.