Identification data filtering prior to addition to MSnExp/MSnSet

lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

http://lgatto.github.io/MSnbase/

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Identification data filtering prior to addition to MSnExp/MSnSet #241

Closed lgatto closed 7 years ago

lgatto commented 7 years ago

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 commented 7 years ago

See new filterIdentificationDataFrame function.

sgibb commented 7 years ago

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.

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lgatto commented 7 years ago

Yep, thanks!