make_h5db_rg: Make and populate a new HDF5 database with red and green...

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

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.

Value

Populates the HDF5 database

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