Description Usage Arguments Value See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | 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()
1 2 | # download test file to temp directory
h5 <- getdb_h5_test(dfp = tempdir())
|
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