CambridgeCentreForProteomics / camprotR

https://cambridgecentreforproteomics.github.io/camprotR/

MIT License

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{ts} silac #7

Closed TomSmithCGAT closed 3 years ago

TomSmithCGAT commented 3 years ago

Adds functions to deal with PD output for SILAC experiments, including extracting information from PSM-level output.

Merging PSM and peptide-level outputs

psm_to_peptide_style_modifications: Updates PSM modifications column so it matches peptide modification column
remove_silac_modifications: Remove SILAC labels from modification column -silac_psm_seq_int

SILAC incorporation rate estimation

get_incorporation: Return incorporation given H & L intensities
plot_incorporation: Plot histogram of peptide/protein SILAC incorporation + annotation

'All-in-one' function for PD output to SILAC incorporation estimation

estimate_incorporation

TomSmithCGAT commented 3 years ago

@csdaw - I've tested this out with a few SILAC incorporation rate tests. E.g from within this repo, the following command works on the command line.

Rscript -e 'camprotR::estimate_incorporation("./raw/SILAC_HandL_bothTags_PSMs.txt", "./raw/SILAC_HandL_bothTags_PeptideGroups.txt", "shared_files/cRAP_FullIdentifiers.fasta", mix=1, outdir="~/test")'

I'm going to test this out with Yagnesh as well now since he was interested in this functionality. If you could look over the above when you have time that would be great. Ultimately, some of this functionality may be better placed in the dedicated infsilac package but I'm happy for it to start off here.

codecov-commenter commented 3 years ago

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