getdb {recountmethylation} | R Documentation |
Combines download and load functions for databases. If the "namematch" argument isn't provided, the latest available file is downloaded. All files include metadata for the available samples.
There are 6 functions. Functions with "h5se" access HDF5-SummarizedExperiment files, and "h5" functions access HDF5 databases. The 4 h5se functions are "rg" (RGChannelSet), "gm" (MethylSet), "gr" (GenomicRatioSet), and "test" (data for 2 samples from "gr"). The 2 h5 functions are "rg" (red and green signal datasets), and "test" (data for 2 samples from "rg"). See vignette for details about file types and classes.
getdb_h5se_test( namematch = "remethdb-h5se_gr-test.*", dfp = NULL, verbose = FALSE ) getdb_h5_test( namematch = "remethdb-h5_rg-test_.*", dfp = NULL, verbose = FALSE ) getdb_h5se_gr(namematch = "remethdb-h5se_gr_.*", dfp = NULL, verbose = FALSE) getdb_h5se_gm(namematch = "remethdb-h5se_gm_.*", dfp = NULL, verbose = FALSE) getdb_h5se_rg(namematch = "remethdb-h5se_rg_.*", dfp = NULL, verbose = FALSE) getdb_h5_rg(namematch = "remethdb-h5_rg_.*", dfp = NULL, verbose = FALSE)
namematch |
Filename pattern to match when searching for database (see defaults). |
dfp |
Folder to search for database file (optional, if NULL then searches cache dir specified by BiocFileCache). |
verbose |
Whether to return verbose messages (default FALSE). |
Either a SummarizedExperiment object for h5se functions, or a file path for h5 functions.
get_rmdl()
# download test file to temp directory h5 <- getdb_h5_test(dfp = tempdir())