search

lgatto / pRolocdata

Data accompanying the pRoloc package
5 stars 5 forks source link

Data from Beltran et al. 2016 #17

Closed lgatto closed 6 years ago

lgatto commented 8 years ago

A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection Pierre M. Jean Beltran, Rommel A. Mathias and Ileana M. Cristea. http://dx.doi.org/10.1016/j.cels.2016.08.012

ococrook commented 6 years ago

This dataset is a time course with 5 times. Each time has paired mock and infected - do we want this has 10 seperate files MSnsets?

lgatto commented 6 years ago

Yes, I suggest we do include all the data, as 10 different MSnSet objects. You can generate the MSnSets yourself, or give me the data (cvs, I presume) and I will create them. The procedure to data in pRolocdata is:

  1. the original data (often from supplementary material) is added to inst/extdata, say newdata_1.csv, newdata_2.csv, ... (the name should be the same as the original file(s)), and the files and provenance is documented in inst/extdata/README. If the data files are really too big, then we might decide not to added them, but they should still be documented in the README file and the script (see point 2) should still assume they are there.
  2. A script, typically called newdata.R or Beltran2016.R, is added to inst/scripts/. That script reads the files above and saves the corresponding (compressed) MSnSet objects directly in data.
  3. Write a man/Beltran2016.Rd documentation file.
  4. Build and check the package and, if successful, send a pull request.
lgatto commented 6 years ago

Done in commit 87dc7ad693513c58cc08c58fc5a764390b02fbc7.

But note: These data are corrupted: some 31 values are formatted as number and dates (see below and here for details). An email has been sent to the authors. In the meantime, these values are set to NA.

2018-03-17-000418_897x213_scrot