NAME

Microarray::Analysis::CGH - A Perl module for analysing CGH microarray data

SYNOPSIS

use Microarray::Analysis::CGH;

my $oData_File = data_file->new($data_file);
my $oCGH = genome_cgh->new($oData_File);

DESCRIPTION

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.

METHODS

flip

Set this parameter to 1 in order to invert the log ratios returned by the data_file object.

Genomic clone locations

embedded_locns

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.

clone_locns_file

Set a Microarray::File::Clone_Locns file object, from which clone locations will be determined.

Data smoothing

do_smoothing

Set this parameter to 1 to perform data smoothing. The Log2 ratios in a window of $window bp are averaged. The window moves in steps of $step bp. Disabled by default.

smooth_window, smooth_step

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 do_smoothing.

SEE ALSO

Microarray, Microarray::Analysis, Microarray::File, Microarray::File::Data_File, Microarray::File::Clone_Locn_File

AUTHOR

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

http://www.instituteforwomenshealth.ucl.ac.uk/AcademicResearch/Cancer/trl

c.jones@ucl.ac.uk

COPYRIGHT AND LICENSE

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.