NAME

Microarray::GEO::SOFT::GPL - GEO platform data class

SYNOPSIS

  use Microarray::GEO::SOFT:
  my $soft = Microarray::GEO::SOFT->new("file" => "GPL15181.soft");
  
  # or you can download from GEO website
  my $soft = Microarray::GEO::SOFT->new;
  $soft->download("GPL15181");
  
  # $gpl is a Microarray::GEO::SOFT::GPL class object
  my $gpl = $soft->parse;
  
  # the meta information
  $gpl->meta;
  $gpl->platform;
  $gpl->title;
  $gpl->field;
  $gpl->accession;
  
  # the platform data is a matrix
  $gpl->matrix;
  # the names for each column
  $gpl->colnames;
  $ the names for each row, it is the primary id for rows
  $gpl->rownames;
  
  # we want to get other ID for microarray data
  my $other_id = $gpl->mapping("miRNA_ID");
  # or
  my $other_id = $gpl->mapping($gpl->colnames[1]);

DESCRIPTION

This module retrieves platform information from microarray data. It is not usually to get platform information from GPL record alone since a GPL record is such a huge file. It is common to get platform information from GSE record.

Subroutines

new("file" = $file)

Initial a GPL class object. The only argument is the microarray data in SOFT format or a file handle that has been openned.

$gpl->parse

Retrieve platform information from microarray data. The platform data in SOFT format is alawys a table

$gpl->meta

Get meta information

$gpl->platform

Get accession number of the platform

$gpl->title

Title of the platform record

$gpl->field

Description of each field in the data matrix

$gpl->accession

Accession number for the platform

$gpl->mapping

get ID mappings

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