search

CambridgeCentreForProteomics / camprotR

https://cambridgecentreforproteomics.github.io/camprotR/
MIT License
4 stars 0 forks source link

Incompatibility issues with add_peptide_positions() #35

Open JosieAC opened 2 years ago

JosieAC commented 2 years ago

https://github.com/CambridgeCentreForProteomics/camprotR/blob/6058ca4acbaf071fc2b0f019adfe7001b043f150/R/ptm.R#L309

add_peptide_positions() is incompatible if using certain version of PD. This is due to inconsistencies in column names. "Sequences" is sometimes "Annotated.Sequences". Please could a customisable parameter be added as with the add_PTM_positions() ?- e.g.:

add_peptide_positions(obj, proteome_fasta, master_protein_col = "Master.Protein.Accessions", 
    sequence_col = "Sequence")