Protein level FDR

[Fredrik Levander]

The current protein assembly function will not attempt calculating FDR at the protein level. It would be useful to perform FDR estimate using the target-decoy principle. Functionality should be when this is enabled: 1) Only use peptides passing the FDR cutoff (as now) 2) Look for decoy prefix in the proteins matching the peptides. If a peptide matches both target and decoy prefixes, the decoy proteins should not be brought forward. 3) Calculate scores by multiplying the FDR of all peptides for all protein. 4) Estimate protein FDR by counting better decoy proteins at all score estimates. 5) Set protein FDR of target proteins 6) Filter protein list so that only proteins with better FDR are reported.

[Fredrik Levander]

(In [3756]) Refs #672. Added protein FDR calculation and filtering. Uppdated form accordingly.

[Fredrik Levander]

(In [3757]) Refs #672. Updated plug-in info.

[Fredrik Levander]

(In [3761]) Fixes #672. Updated help text

[Fredrik Levander]

(In [3774]) Refs #672. Corrected form.

[Fredrik Levander]

(In [3910]) Refs #672. Avoiding rare null pointer exception

[Fredrik Levander]

(In [3912]) Refs #672. Handling spectrum lookup problems.

[Fredrik Levander]

(In [3913]) Refs #672. Handling peptide total intensity of null

[Fredrik Levander]

(In [3914]) Refs #672. Handling peptide total intensity of null

[Fredrik Levander]

(In [4113]) Refs #672. Writing precursor quantity of generated proteins based on included peptides.