Identification data filtering prior to addition to MSnExp/MSnSet

[lgatto]

This is a follow up from #235, that deals specifically with identification data filtering. Default filtering will do the following:

• keep only rank 1 peptides
• remove decoy hits
• keep only unique (proteotypic) peptides

Another important point is that calculateFragments can't handle PEPTIDESEQUENCE1;PEPTIDESEQUENCE2 as input, which will have to be addressed for multi-protein hit peptides and peptides with multiple modifications, although in such cases the sequence might actually be the same.

See also #232

[lgatto]

See new filterIdentificationDataFrame function.

[sgibb]

Just a minor point. This function will fail for `decoy=NULL` and `verbose=TRUE` in the *rank* if-block because `n1` is missing. Same for the other *n* values. Am 7. August 2017 14:22:37 MESZ schrieb Laurent Gatto <notifications@github.com>:

…

Closed #241. -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: #241 (comment)

-- Sent from my mobile device. Please excuse my brevity.

[lgatto]

Yep, thanks!