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Changelog

Source: NEWS.md

pSI 1.2.0

pSI is back on CRAN after being archived in September 2020, when email to the previous maintainer’s address started bouncing. David R. O’Brien, a co-author since version 1.0, is the new maintainer. The five exported functions keep their names, arguments and results; the changes below are packaging and CRAN-policy fixes plus two small bug fixes.

New

  • psi_data() downloads the companion data sets formerly distributed as the pSI.data package (35 mouse bacTRAP cell types and human BrainSpan brain regions) from this package’s GitHub releases, verifies each file’s checksum, and keeps it under tools::R_user_dir("pSI", "cache") only with the user’s consent (otherwise in tempdir()). When offline it returns NULL with a message rather than an error. pSI therefore now requires R >= 4.0.0.

Behavior changes

  • pSI.list() no longer writes CSV files unless asked: write.csv now defaults to FALSE, as the documentation always said and as the other functions already did. CRAN packages may not write to the working directory by default.
  • specificity.index(hist = TRUE) draws the rank histograms on the current graphics device (one page per cell type) instead of writing PNG files into the working directory. The new hist_file argument writes them to a multi-page PDF instead. The device is closed and graphical parameters are restored on exit.
  • candidate.overlap() now compares gene symbols in upper case on both sides, as fisher.iteration() already did. Lower-case (e.g. mouse) candidate symbols previously never matched and silently gave empty overlaps.
  • fisher.iteration(background = "human.mouse") and "mouse.human" download the UCSC kgXref table over HTTPS from hgdownload.soe.ucsc.edu in binary mode (the previous text-mode download produced a corrupt file on Windows) and stop with an informative message if the download fails.

Packaging and documentation

  • gdata is no longer a dependency. The one function used, cbindX(), is replaced by an internal helper with identical output.
  • Authors@R with ORCID for the maintainer; Encoding: UTF-8; URL and BugReports; explicit imports of the base-R functions used; NEWS.md; LICENSE.md; roxygen2-generated documentation and NAMESPACE.
  • Every exported function now documents its return value. Descriptions that said six pSI thresholds now say four, and fisher.iteration() is documented as using Benjamini-Hochberg (not Bonferroni) adjustment, which is what the code has always done.
  • The download URL for the companion data package pSI.data (genetics.wustl.edu) no longer exists and has been removed from the documentation; see the README for where the data live now. Other links were updated to their current locations or replaced by DOIs.

pSI 1.1 (2014-01-30)

CRAN release: 2014-01-30

  • URL to download pSI.data package was added to package documentation to facilitate use of sample mouse & human data and allow for reproducible research.
  • fisher.iteration function now excludes duplicated genes in user supplied candidate gene list.

pSI 1.0 (2014-01-10)

CRAN release: 2014-01-10

  • First CRAN release.