Merge calculateFragments and calculateFragments2 #19
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feat: calculateFragments2 Provides modifications to the generated theoretical fragments
feat: tests for calculateFragments2
Updates based on reviewed PR
Updates according to reviewed PR
Co-authored-by: Sebastian Gibb <[email protected]>
Corrected .cumsumFragmentMasses
Change modified peptide layout into AGC[57.02]AK instead of AG[C]AK to specify the modified mass
Merge branch 'main' of https://github.com/guideflandre/PSMatch # Conflicts: # R/fragments-calculate2.R
sgibb
reviewed
Jan 21, 2025
sgibb
reviewed
Jan 21, 2025
| type <- match.arg(type, choices=c("a", "b", "c", "x", "y", "z"), several.ok=TRUE) | ||
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| if (!is.null(modifications)) { | ||
| warning("'modifications' is deprecated, please use 'fixed_modifications' instead.") |
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Do we need a reminder somewhere to change this into an error in the next release cycle (and remove it in the overnext)?
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Yes, I believe that should prove useful !
sgibb
reviewed
Jan 21, 2025
sgibb
reviewed
Jan 21, 2025
sgibb
reviewed
Jan 21, 2025
lgatto
requested changes
Jan 21, 2025
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I added an issue in Spectra see here issue #346 explaining the potential of a new plotting function and the need for modified |
lgatto
approved these changes
Jan 22, 2025
sgibb
approved these changes
Jan 22, 2025
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This is a quick PR that merges
calculateFragments2intocalculateFragmentsas to avoid redundancy.Documentation is up to date. Unit tests are written and all pass.
I have added a code snippet in
addFragmentsto throw an error if variable modifications have been used:Once this PR is merged, I will create a PR for
plotSpectraandaddFragmentsto include current missing features/fix current errors such as mentioned in #18