getdb {recountmethylation} | R Documentation

## Access database files.

### Description

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.

### Usage

    getdb_h5se_test(
      platform = NULL,
      dfp = NULL,
      namematch = "remethdb-h5se_gr-test.*",
      verbose = FALSE
    )

    getdb_h5_test(
      platform = NULL,
      namematch = "remethdb-h5_rg-test_.*",
      dfp = NULL,
      verbose = FALSE
    )

    getdb_h5se_gr(
      platform = c("hm450k", "epic"),
      dfp = NULL,
      namematch = "remethdb_h5se-gr_.*",
      verbose = FALSE
    )

    getdb_h5se_gm(
      platform = c("hm450k", "epic"),
      dfp = NULL,
      namematch = "remethdb_h5se-gm_.*",
      verbose = FALSE
    )

    getdb_h5se_rg(
      platform = c("hm450k", "epic"),
      dfp = NULL,
      namematch = "remethdb-h5se_rg_.*",
      verbose = FALSE
    )

    getdb_h5_rg(
      platform = c("hm450k", "epic"),
      dfp = NULL,
      namematch = "remethdb-h5_rg_.*",
      verbose = FALSE
    )

### Arguments

`platform` | Valid supported DNAm array platform type. Currently either "epic" for EPIC/HM850K, or "hm450k" for HM450K.
`dfp` | Folder to search for database file (optional, if NULL then searches cache dir specified by BiocFileCache).
`namematch` | Filename pattern to match when searching for database (see defaults).
`verbose` | Whether to return verbose messages (default FALSE).

### Value

Either a SummarizedExperiment object for h5se functions, or a file path for h5 functions.

### See Also

get_rmdl()

### Examples

    h5 <- getdb_h5_test(dfp = tempdir())

[Package recountmethylation version 1.2.3 Index]