get_rmdl: Get DNAm assay data.

In recountmethylation: Access and Analyze DNA Methylation Array Databases

Description

Uses RCurl to recursively download latest H5SE and HDF5 data objects from the server. This is currently wrapped in the getdb() functions.

Usage

get_rmdl(
  which.class = c("rg", "gm", "gr", "test"),
  which.type = c("h5se", "h5"),
  fn = NULL,
  dfp = "downloads",
  url = "https://recount.bio/data/",
  show.files = FALSE,
  download = TRUE,
  verbose = TRUE,
  sslver = FALSE
)

Arguments

which.class	Either "rg", "gm", "gr", or "test" for RGChannelSet, MethylSet, GenomicRatioSet, or 2-sample subset (default "test").
which.type	Either "h5se" for an HDF5-SummarizedExperiment (default) or "h5" for an HDF5 database.
fn	Name of file on server to download (optional, default NULL).
dfp	Download destination directory (default "downloads").
url	The server URL to locate files for download.
show.files	Whether to print server file data to console (default FALSE).
download	Whether to download (TRUE) or return queried filename (FALSE).
verbose	Whether to return verbose messages.
sslver	Whether to use server certificate check (default FALSE).

Value

New filepath to dir with downloaded data.

See Also

servermatrix(), getURL(), loadHDF5SummarizedExperiment(), h5ls()

recountmethylation documentation built on Nov. 8, 2020, 4:59 p.m.