/ 
TRL-Microarray-0.061
/ TRL::Microarray::Feature

NAME

TRL::Microarray::Feature - A Perl module for creating and manipulating microarray feature objects

SYNOPSIS

use TRL::Microarray;

my $feature = array_feature->new('feature 1');
$feature->add_feature_spot($spot);

DESCRIPTION

TRL::Microarray::Feature is an object-oriented Perl module for creating and manipulating microarray feature objects. It serves as a container into which you place spot objects that are replicates of the same genetic feature, and returns average information about those spots.

METHODS

feature_id

Name of the feature

genetic_data

An object containing relevant genetic data. For example, in a CGH microarray experiment this would be a TRL::BAC_Clone object

get_feature_spots

Returns a list of spot objects attributed to a feature

get_feature_replicates

Returns the number of spots attributed to a feature

spots_passed_qc

Returns the number of spots that passed QC criteria and are included in the feature data

mean_ch1 and mean_ch2

Mean signal of all spots representing a feature

mean_ratios and mean_log_ratios

Calculates the ratio (or log2 ratio) between the two signal channels for each replicate, and returns the mean of those values

ratio_means and log_ratio_means

Calculates the mean of the replicate signals for each channel, and returns their ratio (or log2 ratio)

SEE ALSO

TRL::Microarray, TRL::Microarray::Spot

AUTHOR

Christopher Jones, Translational Research Laboratories, Institute for Women's Health, University College London.

c.jones@ucl.ac.uk

COPYRIGHT AND LICENSE

Copyright 2006 by Christopher Jones, University College London

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.