pepXMLTab error reading Mascot pepXML file
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@laurafancello-22293
Last seen 2.2 years ago

I exported from Mascot GUI a pepXML file and I tried to read it using the pepXMLTab R package:

library(pepXMLTab)
options(stringsAsFactors=FALSE)
pepXMLTab <- pepXMLTab::pepXML2tab(pepxml="F134048.xml")

but I got this error:

Error in (function (..., deparse.level = 1, make.row.names = TRUE, stringsAsFactors = default.stringsAsFactors(), : numbers of columns of arguments do not match

Do you have any idea of why this does not work? In principle my pepXML file should be a valid one since I was able to convert it to a .tsv using this tool: http://wlab.ethz.ch/tools/

Are there any compatibility issues between pepXMLTab and Mascot-generated pepXML files? Are there some options I had to set when exporting Mascot file to make it suitable to pepeXMLTab?

Thank you!

This is my sessionInfo():

R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)
Matrix products: default
locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252 LC_NUMERIC=C                   LC_TIME=French_France.1252    
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] pepXMLTab_1.18.0
loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1    XML_3.98-1.20*
pepXMLTab Mascot pepXML file • 182 views
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