Zuguang Gu > Microarray-GEO-SOFT-0.20 > Microarray::GEO::SOFT::GSE

Download:
Microarray-GEO-SOFT-0.20.tar.gz

Dependencies

Annotate this POD

View/Report Bugs
Source  

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->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 ^

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.

Subroutines

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.

$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

disabled

$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

disabled

$gse->colnames

disabled

$gse->colnames_explain

disabled

$gse->matrix

disabled

$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.

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.

SEE ALSO ^

Microarray::GEO::SOFT

syntax highlighting: