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martinry / proteasy

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I've hundreds of peptides, one protein #1

Closed Dmorgen closed 1 year ago

Dmorgen commented 1 year ago

Hi, how do I run the code looking for proteases based on peptide sequences, for just one protein? the script wants the peptide and protein vector to have the same lengths...

martinry commented 1 year ago

Hi, repeat the protein accession in a vector for as many peptide sequences you have.

peptide <- c("FEEVSGNVSPGTR", "FVSETESR", "LLVVYPW", "ITLLSAL")
protein <- rep("P02671", length(peptide))
res <- findProtease(protein = protein, peptide = peptide, organism = "Homo sapiens")
Dmorgen commented 1 year ago

Thanks! another question - iI've couple of dozens of protein uniprot accessions that give an error that they couldn't be mapped. is there a way to add to the "findProtease" command to ignore positions in both vectors that could not be mapped? thanks!

martinry commented 1 year ago

The function gives a warning that the accessions can not be mapped. These accessions and corresponding peptide sequences are automatically excluded from the search. So as I understand you, the default behavior is already what you requested.

Dmorgen commented 1 year ago

Thanks! D.

From: Martin Rydén @.> Sent: Monday, March 20, 2023 6:43 PM To: martinry/proteasy @.> Cc: David Morgenstern @.>; Author @.> Subject: Re: [martinry/proteasy] I've hundreds of peptides, one protein (Issue #1)

The function gives a warning that the accessions can not be mapped. These accessions and corresponding peptide sequences are automatically excluded from the search. So as I understand you, the default behavior is already what you requested.

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