As a part of this issue, we want to add a converter from Metamorpheus to MSstatsPTM format.
Changes
Added a new MetamorpheusToMSstatsPTMFormat function
Given there can be multiple modifications on a given peptide in Metamorpheus' output, we will initially set up the converter such that the user targets a specific modification, e.g. "Common Biological:Phosphorylation on S", using the parameter mod_id.
For now, we will neither remove rows containing a peptide with multiple modifications nor allow users to track multiple modifications (e.g. ProteinId_C_148_S_157). We can always add that feature in the future as an enhancement.
Testing
Added unit test that verifies that PTM and Protein output are produced with greater than 0 rows.
Ran R check and generated no new errors or warnings.
[ ] Any dependent changes have been merged and published in downstream modules - requires MSstatsConvert function MetamorpheusToMSstatsFormat to be published to Bioconductor.
Motivation and Context
As a part of this issue, we want to add a converter from Metamorpheus to MSstatsPTM format.
Changes
mod_id
.Testing
Checklist Before Requesting a Review
MetamorpheusToMSstatsFormat
to be published to Bioconductor.