get_rmdl: Get DNAm assay data.

In metamaden/recountmethylation: Access and analyze public DNA methylation array data compilations

Get DNAm assay data.

Description

Uses RCurl to download the latest HDF5-SummarizedExperiment or HDF5 database compilation files objects from the server. Calls servermatrix and performs various quality checks to validate files and downloads. This function is wrapped in the getdb() set of functions (type '?getdb' for details).

Usage

get_rmdl(
  which.class = c("rg", "gm", "gr", "test"),
  which.type = c("h5se", "h5"),
  which.platform = c("hm450k", "epic"),
  fn = NULL,
  dfp = "downloads",
  url = "https://methylation.recount.bio/",
  show.files = FALSE,
  download = TRUE,
  sslver = FALSE,
  verbose = TRUE
)

Arguments

which.class	Either "rg", "gm", "gr", or "test" for RGChannelSet, MethylSet, GenomicRatioSet, or 2-sample subset.
which.type	Either "h5se" for an HDF5-SummarizedExperiment or "h5" for an HDF5 database.
which.platform	Supported DNAm array platform type. Currently supports either "epic" for EPIC/HM850K, or "hm450k" for HM450K.
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).
sslver	Whether to use server certificate check (default FALSE).
verbose	Whether to return verbose messages (default TRUE).

Value

New filepath to dir containing the downloaded data.

See Also

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

Examples

# prints file info from server:
path <- try(get_rmdl(which.class = "test", which.type = "h5se", 
show.files = TRUE, download = FALSE))

metamaden/recountmethylation documentation built on Jan. 5, 2023, 9:56 a.m.