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compomics / peptide-shaker-2.0-issue-tracker

Issue tracker for the beta release of PeptideShaker 2.0
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The possible sequence coverage values ought to be checked #32

Closed hbarsnes closed 4 years ago

hbarsnes commented 5 years ago

The values provided for the possible sequence coverage ought to be checked as they do not match the manually calculated values. They have also dropped around 10% compared to the old version. (Which also do not match the manually calculated values btw...)

hbarsnes commented 4 years ago

The source of the issue is that while ProteinUtils.getObservableAminoAcids is used for the possible coverage value shown above the coverage plot and in the coverage column in the protein table, the coverage plot itself is based on the estimateCoverableAA method in IdentificationFeaturesGenerator.

The former only calculates if the given amino acid can be detected or not given the enzyme and peptide lengths (it does not seem to care about the minimum peptide length though?), while the latter returns a probability per residue.

The situation is further complicated due to a quick fix in the updateSequenceCoverage method in OverviewPanel (search for "transparentIndex") which hides all coverable residues if the probability is less than 0.01. As otherwise everything that is not covered by detected peptides would show up as gray.

@mvaudel Not sure what is the best way to make this all more consistent..?

hbarsnes commented 4 years ago

Fix: An explanation of what the possible coverage means has now been added to the help text.