NAME
Microarray::GEO::SOFT::GSE - GEO series data class
SYNOPSIS
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->field;
$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->[0];DESCRIPTION
This module retrieves data storing as GEO series format.
Subroutines
new("file" = $file)-
Initial a GSE class object. The only argument is the microarray data in SOFT format or a file handle that has been openned.
$gse->parse-
Retrieve series information from microarray data.
$gse->meta-
Get meta information
$gse->platform-
Get accession number of the platform
$gse->title-
Title of the platform record
$gse->field-
Description of each field in the data matrix
$gse->accession-
Accession number for the platform
$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.
$gse->merge-
merge single GSMs into a expression value matrix. The merging process is by platforms. Each matrix is a GDS class object.
AUTHOR
Zuguang Gu <jokergoo@gmail.com>
COPYRIGHT AND LICENSE
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.