Bio::MaxQuant::ProteinGroups::Response - Analyze MQ proteinGroups for differential responses
Version 0.01
This module is tailored for MaxQuant data, but could be applicable elsewhere. The target experiment is one where several celltypes have been assayed for responses to different conditions, e.g. cancer cell lines responding to hormones and drugs. The module help to analyse responses to the conditions within each cell line and differences in those responses between cell lines. Those differences in responses indicate that the proteins involved are markers of the mechanism by which the cells differ in their response, and are therefore not only good targets to exploit for biomarkers, but also for biological follow up.
use Bio::MaxQuant::ProteinGroups::Response; my $resp = Bio::MaxQuant::ProteinGroups::Response->new( filepath=>'proteinGroups.txt' ); $resp->replicate_comparison(output_directory=>'./replicate_comparisons'); $resp->calculate_response_comparisons(output_directory=>'./responses'); $resp->calculate_differential_response_comparisons(output_directory=>'./differential_responses');
The data are output as tables in the directories. They are the printable tables returned from Statistics::Reproducibility.
creates a new ProteinGroups object.
Options: filepath - path to the file! default is proteinGroups.txt separator - NOT table separator! This is the separator used in the experiment name to separate cellline from condition from replicate. Default is full stop (period) rseparator - used for separating the compared cells/conditions. the default is hyphen (-) replicate_indicator - used in differential response comparisons to indicate which cell the individual replicates were compared (with the median of the other cell)
Returns the list of experiments in the file as a hash. Keys are names, values are listrefs of cellline,condition,replicate. Caches! So once called, it will not re-read the file unless/until you delete $o->{experiments}
Also populates cellines, conditions and replicates lists, which are accessible by their own accessors.
Returns the list of cell lines. Ensures experiments() is called.
Returns the list of conditions. Ensures experiments() is called.
Returns a hash of key=conditions, value=list of replicates. Ensures experiments() is called.
Returns the list of replicates. Ensures experiments() is called.
Method to parse the experiment name. Uses $o->{separator} to separate into 3 parts. Uses index and substr, not regexes. Default separator is dot/fullstop/period "." .
Method to parse the response name. Uses $o->{rseparator} to separate into 3 parts. Uses index and substr, not regexes. Default separator is hyphen "-", which should not be used in experiment name!
Uses Statistics::Reproducibility to get normalized values and metrics on each condition.
Caches!
Returns the list of comparisons that can be made between conditions within each cell line, given the replicates available.
At least 2 replicates must be available for a comparison to be made.
Caches.
Returns the list of comparisons that can be made between cell line responses to a each condition.
Reads in all the protein ratios from the proteinGroups file. Also reads other identifying information, such as id and Leading Proteins. Reads each non-normalized ratio column into a list and stores them in a hash by experiment name.
Converts one datum into a logged ratio or an empty string, depending.
calculates the differences between conditions in a cell type. outputs a bunch of files. You can specify the diretory with output_directory option.
calculates the medians for all replicate sets and stores them in $0->{medians}
helper function that does a simple median calculation
Calls:
my $results = Statistics::Reproducibility ->new() ->data($data) ->run() ->printableTable($depth);
for each comparison.
But first I need to calculate the comparisons... i.e. take logs and subtract!
Jimi, <j at 0na.me>
<j at 0na.me>
Please report any bugs or feature requests to bug-bio-maxquant-proteingroups-response at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-MaxQuant-ProteinGroups-Response. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
bug-bio-maxquant-proteingroups-response at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc Bio::MaxQuant::ProteinGroups::Response
You can also look for information at:
RT: CPAN's request tracker (report bugs here)
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-MaxQuant-ProteinGroups-Response
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Bio-MaxQuant-ProteinGroups-Response
CPAN Ratings
http://cpanratings.perl.org/d/Bio-MaxQuant-ProteinGroups-Response
Search CPAN
http://search.cpan.org/dist/Bio-MaxQuant-ProteinGroups-Response/
Copyright 2014 Jimi.
This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:
http://www.perlfoundation.org/artistic_license_2_0
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To install Bio::MaxQuant::ProteinGroups::Response, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MaxQuant::ProteinGroups::Response
CPAN shell
perl -MCPAN -e shell install Bio::MaxQuant::ProteinGroups::Response
For more information on module installation, please visit the detailed CPAN module installation guide.