NEWS

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mspms 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.