NAME

getIonIntensities.pl - Extraction of ion intensities information from a .peptSpectra.xml file

SYNOPSIS

getIonIntensities.pl --pept=peptfile [options]

OPTIONS

Use getIonIntensities.pl -h

DESCRIPTION

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.

EXAMPLE

./getIonIntensities.pl --pept=example.peptSpectra.xml -rformat -withplots > intensities.dataf

AUTHOR

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.

	Global
`s`	Focus search bar
`?`	Bring up this help dialog

	GitHub
`g` `p`	Go to pull requests
`g` `i`	go to github issues (only if github is preferred repository)

	POD
`g` `a`	Go to author
`g` `c`	Go to changes
`g` `i`	Go to issues
`g` `d`	Go to dist
`g` `r`	Go to repository/SCM
`g` `s`	Go to source
`g` `b`	Go to file browse

	Search terms
module: (e.g. module:Plugin)
distribution: (e.g. distribution:Dancer auth)
author: (e.g. author:SONGMU Redis)
version: (e.g. version:1.00)