Microarray::GEO::SOFT::GSE - GEO series data class
use Microarray::GEO::SOFT: my $soft = Microarray::GEO::SOFT->new("file" => "GSE35505.soft"); # or you can download from GEO website my $soft = Microarray::GEO::SOFT->new; $soft->download("GSE35505"); # $gse is a Microarray::GEO::SOFT::GSE class object my $gse = $soft->parse; # the meta information $gse->meta; $gse->platform; $gse->title; $gse->accession; # since a GSE can contain more than one GSM and GPL, so the GPL and GSM stored # in GSE is a list or array my $samples = $gse->list("GSM"); my $platforms = $gse->list("GPL"); # data in single GSM can be merged as matrix by platforms # it is a GDS class object my $g = $gse->merge->;
A Series record links together a group of related Samples and provides a focal point and description of the whole study. Series records may also contain tables describing extracted data, summary conclusions, or analyses. Each Series record is assigned a unique and stable GEO accession number (GSExxx). (Copyed from GEO web site).
This module retrieves data storing as GEO series format.
new("file" => $file, "verbose" =1)>
Initial a GSE class object. The only argument is the microarray data in SOFT format or a file handle that has been openned. The argument is optional and the platform can be download through Microarray::GEO::SOFT. 'verbose' determines whether print the message when analysis. 'sample_value_column' is the column name for table data when parsing GSM data.
Get meta information
Set meta information. Valid argumetns are 'accession', 'title' and 'platform'.
Accession number for the platform the series belong to. Note here the platform is an array reference.
Title of the series record
Accession number for the series
$gse->list("GSM" | "GPL")
Since a series can contain more than one samples and platforms. This method can get GSM list or GPL list that belong to the GSE record.
Set the GSM and GPL list to GSE object. Valid arguments are 'GPL' and 'GSM'.
merge single GSMs into a expression value matrix. The merging process is by platforms. Each matrix is a GDS class object.
Zuguang Gu <email@example.com>
Copyright 2012 by Zuguang Gu
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.12.1 or, at your option, any later version of Perl 5 you may have available.