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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,
  keep_only_preop_and_3months = TRUE,
  keep_only_complete_time_points = TRUE
)

Arguments

dest_dir

Directory where the dataset should be saved

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_* arguments, so please use force = TRUE if you change the keep_only_* settings.

keep_only_CPMG_1r

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

keep_only_preop_and_3months

If TRUE, keep only the preoperatory and the "three months after surgery" time points, enough for the tutorial

keep_only_complete_time_points

If TRUE, remove samples that do not appear on all 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 three logical parameters to limit the amount of downloaded/saved data. To run the tutorial workflow:

  • only the "preop" and "three months" timepoints are used,

  • only subjects measured in both preop and three months time points are used

  • only the CPMG samples are used.

If you want to run the tutorial, you can set those filters to TRUE. Then, roughly 800MB will be downloaded, and 77MB of disk space will be used, since for each downloaded sample we remove all the data but the CPMG.

If you set those filters to FALSE, roughly 1.8GB of data will be downloaded (since we have more timepoints to download) and 1.8GB of disk space will be used.

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 in the FTP 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
} # }