getdb: Access database files.

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

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())

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