Changes in version 0.99                         

mspms 0.99.0

  - Initial Bioconductor submission.

mspms 0.99.1

  - Major edits to the structure of the package based on review. Now
    utilizes QFeatures objects and MSCoreutils to perform data
    processing steps.

mspms 0.99.2

  - Removed logo from vignette to pass Bioconductor build. Fixed bugs to
    nterm_cleavages() and cterm_cleavages() that were causing problems
    when n_residue != 4. Simplified the logic behind these functions and
    added extensive testing to confirm that they work as expected with a
    range of peptide sequences. Minor change to the plot_volcano()
    function allowing the user to specify a padj threshold.

mspms 0.99.3

  - Removed some redundant tests of the log2fc_t_test() function that
    took a long time to perform and were causing timeouts on the
    Bioconductor build.

mspms 0.99.4

  - Removed the cathepsin B-D data from the internal datasets and from
    extdata/ . This keeps the example run time down, as well as greatly
    reduces the overall size of the package.

mspms 0.99.5

  - Removed interactive heatmap from vignette to get rid of warning that
    vignette size was too large. Minor changes to vignette aesthetics.

mspms 0.99.6

  - Improved vignette according to review feedback. Added peptide length
    calculation to row data.

mspms 0.99.7

  - Added ability to remove dendrogram plotting from plot_heatmap().
    This was done because the dendrogram plotting feature in heatmaply
    is recursive and uses a ton of memory which was problematic for the
    shiny instance.

mspms 0.99.8

  - Added support for limma based statistics via limma_stats() function

mspms 1.1.0

  - Added support for DIA-NN report.pr_matrix.tsv output.

mspms 1.1.1

  - Fixed a bug where rownames in the QFeatures object could be
    misaligned due to a mismatch in the order of colData compared to
    prepared_data. Fixed by changing the order of the colData to be the
    order of the prepared data before reading as a QFeatures object

mspms 1.3.1

  - Improvements in response to reviewer comments after BMC
    Bioinformatics submission.

1.  Added prepare_sage() to support results from Sage search engine.
2.  Refactored prepare_* functions to prevent unnecessary duplication of
    code.
3.  Refactored nterm_cleavage and cterm_cleavage to prevent unnecessary
    duplication of code.
4.  Refactored code to reduce duplication in the check_* functions
5.  Fixed t-testing which was inadvertently performing t-tests on
    reverse log2 transformed values.