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Download MTBLS242

Source: R/download_MTBLS242.R
download_MTBLS242.Rd

Downloads the MTBLS242 dataset from Gralka et al., 2015. DOI: doi:10.3945/ajcn.115.110536 .

Usage

download_MTBLS242(
  dest_dir = "MTBLS242",
  force = FALSE,
  keep_only_CPMG_1r = TRUE,
  timepoints = c("preop", "12 months after surgery"),
  keep_only_complete_time_points = TRUE
)

Arguments

dest_dir

Directory where the dataset should be saved. Every freshly downloaded file is verified against the canonical SHA-256 checksums MetaboLights publishes for MTBLS242. As a fallback for when that manifest cannot be fetched, the SHA-256 of every downloaded file is also pinned to <dest_dir>/SHA256SUMS the first time it is saved, and re-verified on every later call that reuses a cached file, so local corruption or tampering between calls is detected either way.

force

Logical. If TRUE we do not re-download files if they exist. The function does not check whether cached versions were downloaded with different keep_only_*/timepoints arguments, so please use force = TRUE if you change those settings. force = TRUE also re-downloads and re-pins the checksum of every file, rather than verifying it against a previously pinned value. If you only added timepoints (kept every previously requested one), deleting <dest_dir>/sample_annotations.tsv before calling again is enough to pick up the new timepoints without re-downloading previously cached samples.

keep_only_CPMG_1r

If TRUE, remove all other data beyond the CPMG real spectrum, which is enough for the tutorial

timepoints

Either NULL to keep every timepoint, or a character vector with the TimePoint values to keep (a subset of "preop", "3 months after surgery", "6 months after surgery", "9 months after surgery", "12 months after surgery"). Defaults to c("preop", "12 months after surgery"), enough for the tutorial.

keep_only_complete_time_points

If TRUE, remove samples that do not appear on all of the kept timepoints. Useful for the tutorial.

Value

Invisibly, the annotations. See the example for how to download the annotations and create a dataset from the downloaded files.

Details

Besides the destination directory, this function includes parameters to limit the amount of downloaded/saved data. To run the tutorial workflow with a two-timepoint comparison:

  • only the requested timepoints (e.g. "preop" and "12 months after surgery") are used,

  • only subjects measured in all of the requested timepoints are used,

  • only the CPMG samples are used.

The full study has five timepoints: "preop", "3 months after surgery", "6 months after surgery", "9 months after surgery", and "12 months after surgery". Restricting timepoints to two of them keeps the download small (roughly 800MB downloaded, 77MB on disk with keep_only_CPMG_1r = TRUE). Passing timepoints = NULL downloads every timepoint (roughly 1.8GB downloaded and on disk).

Note that we have experienced some sporadic timeouts from Metabolights, when downloading the dataset. If you get those timeouts simply re-run the download function and it will restart from where it stopped.

Note as well, that we observed several files to have incorrect data:

  • Obs4_0346s.zip is not present on the server

  • Obs0_0110s.zip and Obs1_0256s.zip incorrectly contain sample Obs1_0010s

This function removes all three samples from the samples annotations and doesn't download their data.

Examples

if (FALSE) { # \dontrun{
  download_MTBLS242("./MTBLS242")
  annot <- readr::read_tsv(annotations_destfile)

  dataset <- nmr_read_samples(annot$filename)
  dataset <- nmr_meta_add(dataset, annot)
  dataset
} # }