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tvpham / iq

An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
BSD 3-Clause "New" or "Revised" License
19 stars 9 forks source link

Issue with the peptide_extractor #14

Open SamDCalis opened 3 months ago

SamDCalis commented 3 months ago

Hi all,

I'm currently processing an LFQ-DiaNN output using the iq package. My code below works fine except that the peptide_extractor worked once but then stopped working the next day. Any ideas why? Thanks in advance.

iq::process_long_format(file.path(pathTotxt, Reportfile), output_filename = paste0(pathTotxt,"/proteinGroups_iqfiltered.tsv"), filter_double_less = c("Lib.Q.Value" = "0.01", "Lib.PG.Q.Value" = "0.01"), annotation_col = c("Protein.Names", "Genes"), intensity_col = "Fragment.Quant.Raw", show_boxplot = F ,peptide_extractor = function(x) gsub("[0-9].*$", "", x) ) R version: 4.2.2 Rstudio 2023.06.0+421

tvpham commented 2 months ago

Hi, your code works with the example data used in the README https://github.com/tvpham/iq/releases/download/v1.1/report.zip. If you share (part of) the data, perhaps I can have a quick check.

Thang

SamDCalis commented 2 months ago

Looks like it was just a temporary issue because it works fine now indeed. Thanks for looking into it.