Microarray::Analysis::CGH - A Perl module for analysing CGH microarray data
use Microarray::Analysis::CGH; my $oData_File = data_file->new($data_file); my $oCGH = genome_cgh->new($oData_File);
Microarray::Analysis::CGH is an object-oriented Perl module for analysing CGH microarray data from a scan data file, for sorting the reporters in a single chromosome or whole genome context, and to apply smoothing.
By setting the
embedded_locns parameter to 1, the module expects the reporter name to be in the 'ID' field of the data file (i.e. the
synonym_id() of the
data_file object) and the clone location to be present in the 'Name' field of the data file (i.e. the
feature_id() of the
data_file object). The clone location should be of the notation 'chr1:12345..67890'. When using
embedded_locns a clone position file is not required. Disabled by default.
Set a Microarray::File::Clone_Locns file object, from which clone locations will be determined.
Set this parameter to 1 to perform data smoothing. The Log2 ratios in a window of
$windowbp are averaged. The window moves in steps of
$stepbp. Disabled by default.
Set the desired window and step sizes for smoothing using these two parameters. A default window size of 500,000bp and step size of 150,000bp provide a moderate level of smoothing, removing outliers while preserving short regions of copy number change. Setting either of these parameters will invoke the smoothing process without setting
Christopher Jones, Gynaecological Cancer Research Laboratories, Institute for Women's Health, University College London.
Copyright 2008 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.