getIonIntensities.pl - Extraction of ion intensities information from a .peptSpectra.xml file
getIonIntensities.pl --pept=peptfile [options]
Use getIonIntensities.pl -h
The script parses a collection of trusted peptide/spectrum matches stored in a .peptSpectra.xml file to extract statistics regarding fragment ion intensities. It is possible to output the results either in text format (default) or in a format readable by R. In the latter case, the simple R script, ionStat.R, can be used for plotting data.
In addition, plots can be generated for each match found in the .peptSpectra.xml file(s) by using the -withplots.
./getIonIntensities.pl --pept=example.peptSpectra.xml -rformat -withplots > intensities.dataf
Jacques Colinge
To install InSilicoSpectro, copy and paste the appropriate command in to your terminal.
cpanm
cpanm InSilicoSpectro
CPAN shell
perl -MCPAN -e shell install InSilicoSpectro
For more information on module installation, please visit the detailed CPAN module installation guide.