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[WIP] Comparison fdr #30

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[WIP] Comparison fdr #30

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Commits on Jul 1, 2022

  1. update mappings to separate contaminants

    @benpullman
    benpullman committed Jul 1, 2022
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Commits on Jul 6, 2022

  1. use variants

    @benpullman
    benpullman committed Jul 6, 2022
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  2. add non-numeric filter to PE column

    @benpullman
    benpullman committed Jul 6, 2022
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  3. update variant definition to be sum of integer mod masses

    @benpullman
    benpullman committed Jul 6, 2022
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Commits on Jul 7, 2022

  1. find best cosine over all sequences matching

    @benpullman
    benpullman committed Jul 7, 2022
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  2. update to only calculate precursor FDR for spectra that pass PSM FDR

    @benpullman
    benpullman committed Jul 7, 2022
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  3. properly account for PSM quality filters

    @benpullman
    benpullman committed Jul 7, 2022
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  4. use EI as tie breaker when PSM scores are the same

    @benpullman
    benpullman committed Jul 7, 2022
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  5. keep track of num PSMs

    @benpullman
    benpullman committed Jul 7, 2022
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  6. keep track of overall best PSM score

    @benpullman
    benpullman committed Jul 7, 2022
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  7. keep track of num_precursors per variant

    @benpullman
    benpullman committed Jul 7, 2022
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  8. add variant number, option to run with peptidoforms and not variants

    @benpullman
    benpullman committed Jul 7, 2022
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  9. assume TMT

    @benpullman
    benpullman committed Jul 7, 2022
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  10. fix variant aggregation

    @benpullman
    benpullman committed Jul 7, 2022
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  11. cosine updates

    @benpullman
    benpullman committed Jul 7, 2022
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  12. update variant grouping

    @benpullman
    benpullman committed Jul 7, 2022
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Commits on Jul 8, 2022

  1. update PSM counting

    @benpullman
    benpullman committed Jul 8, 2022
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Commits on Jul 10, 2022

  1. update outputs to be better named

    @benpullman
    benpullman committed Jul 10, 2022
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Commits on Jul 12, 2022

  1. update to fix bug in EI representative

    @benpullman
    benpullman committed Jul 12, 2022
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Commits on Jul 15, 2022

  1. update peptide protein cosine

    @benpullman
    benpullman committed Jul 15, 2022
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Commits on Aug 5, 2022

  1. changes for window filters

    @benpullman
    benpullman committed Aug 5, 2022
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Commits on Aug 12, 2022

  1. changes to add FDR to comparison, should be discarded

    @benpullman
    benpullman committed Aug 12, 2022
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