| Title: | Example 1d NMR Data for Metabolic Profiling |
|---|---|
| Description: | Provides example one-dimensional proton NMR spectra of murine urine samples collected before and after bariatric or sham surgery (Roux-en-Y gastric bypass). The data are adapted from Jia V Li et al. (2011), "Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk", Gut, 60(9), 1214–1223. <doi:10.1136/gut.2010.234708>. This package serves as example data for metabolomics analysis and teaching purposes. |
| Authors: | Torben Kimhofer [aut, cre] (ORCID: <https://orcid.org/0000-0001-7158-9930>) |
| Maintainer: | Torben Kimhofer <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.2.0 |
| Built: | 2026-10-10 11:20:05 UTC |
| Source: | https://github.com/bioc/nmrdata |
Retrieves the raw NMR experiment archive (tar.gz) from ExperimentHub and ensures it is unpacked once into a cache directory. If the unpacked directory already exists and contains files, it is reused; otherwise the tarball is extracted. Optionally, an existing unpack can be forced to be replaced.
getRawExpDir(quiet = FALSE, reuntar = FALSE, tar_override = NULL)getRawExpDir(quiet = FALSE, reuntar = FALSE, tar_override = NULL)
quiet |
Logical; suppress progress messages (default |
reuntar |
Logical; force re-extraction even if the directory already
exists and is populated (default |
tar_override |
Character path to a local |
This helper is idempotent: repeated calls return the same normalized path without re-downloading or re-unpacking, unless explicitly instructed.
The function always uses the same internal ExperimentHub ID
(EH9906 by default in this package).
The tarball is retrieved via ExperimentHub::ExperimentHub().
The directory is created next to the cached tarball inside the EH cache.
If the archive contains exactly one top-level folder, that name is reused.
Otherwise a default folder name ("nmrdata") is created.
A character scalar: normalized absolute path to the unpacked dataset directory inside the local ExperimentHub cache.
ExperimentHub::ExperimentHub(), utils::untar()
td <- tempfile(); dir.create(td) dir.create(file.path(td, "tinydata")) cat("ex data\n", file = file.path(td, "tinydata", "a.txt")) tarfile <- file.path(td, "tinydata.tar.gz") utils::tar(tarfile, files = "tinydata", compression = "gzip", tar = "internal") p <- getRawExpDir(tar_override = tarfile, quiet = TRUE) basename(p) # "tinydata" list.files(p) # "a.txt" ## Not run: exp_dir <- getRawExpDir() list.files(exp_dir, recursive = TRUE)[1:5] # Force re-unpack if you think the folder is corrupted exp_dir <- getRawExpDir(reuntar = TRUE) ## End(Not run)td <- tempfile(); dir.create(td) dir.create(file.path(td, "tinydata")) cat("ex data\n", file = file.path(td, "tinydata", "a.txt")) tarfile <- file.path(td, "tinydata.tar.gz") utils::tar(tarfile, files = "tinydata", compression = "gzip", tar = "internal") p <- getRawExpDir(tar_override = tarfile, quiet = TRUE) basename(p) # "tinydata" list.files(p) # "a.txt" ## Not run: exp_dir <- getRawExpDir() list.files(exp_dir, recursive = TRUE)[1:5] # Force re-unpack if you think the folder is corrupted exp_dir <- getRawExpDir(reuntar = TRUE) ## End(Not run)