make_h5db_rg: Make and populate a new HDF5 database with red and green...
In metamaden/rmpipeline: Process DNAm array IDATs into database files

make_h5db_rg

R Documentation

Make and populate a new HDF5 database with red and green signal, and metadata

Description

Make and populate a new HDF5 database with red and green signal, and metadata

Usage

make_h5db_rg(
  dbfnstem,
  dbpath,
  version,
  ts,
  fnpath,
  platform = c("hm450k", "epic"),
  fnl,
  dsnl = c("redsignal", "greensignal"),
  rmoldh5 = TRUE,
  newtables = FALSE,
  mdpath = NULL,
  ngsm.block = 50,
  verbose = TRUE
)

Arguments

`dbfnstem`	Stem of filename for h5 database (to which ts and version appended)
`dbpath`	Database file path to write to.
`version`	Version of new database file.
`ts`	Timestamp of new database file.
`fnpath`	Path to dir containing files in fnl.
`platform`	DNAm array platform for instance.
`fnl`	Vector of signal tables containing data to be added.
`dsnl`	Vector of new h5 data set objects in the h5db object, corresponding (1:1) to the files declared in fnl.
`newtables`	Whether to also add new data tables (noob-norm. Beta-values, meth. and unmeth. signal).
`mdpath`	If addmd, the path to the metadata file to load.
`ngsm.block`	Number of GSMs (samples) per process block (default 50, passed to 'h5_newtables()').
`verbose`	Whether to show verbose status updates.