get_rmdl {recountmethylation} | R Documentation

## 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))

[Package recountmethylation version 1.2.3 Index]