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->[0];
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" =
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.
$gse->parse
Retrieve series information. This subroutine extracts the basic meta information and the Microarray::GEO::SOFT::GSM list and the Microarray::GEO::SOFT::GPL list
$gse->meta
Get meta information
$gse->set_meta(HASH)
Set meta information. Valid argumetns are 'accession', 'title' and 'platform'.
$gse->table
disabled
$gse->set_table
$gse->platform
Accession number for the platform the series belong to. Note here the platform is an array reference.
$gse->title
Title of the series record
$gse->accession
Accession number for the series
$gse->rownames
$gse->colnames
$gse->colnames_explain
$gse->matrix
$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->set_list(HASH)
Set the GSM and GPL list to GSE object. Valid arguments are 'GPL' and 'GSM'.
$gse->merge
merge single GSMs into a expression value matrix. The merging process is by platforms. Each matrix is a GDS class object.
Zuguang Gu <jokergoo@gmail.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.
Microarray::GEO::SOFT
To install Microarray::GEO::SOFT, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Microarray::GEO::SOFT
CPAN shell
perl -MCPAN -e shell install Microarray::GEO::SOFT
For more information on module installation, please visit the detailed CPAN module installation guide.