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



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


  use Microarray::GEO::SOFT:
  my $soft = Microarray::GEO::SOFT->new("file" => "GPL15181.soft");
  # or you can download from GEO FTP site
  my $soft = Microarray::GEO::SOFT->new;
  # since you use a GPL id
  # $gpl is a Microarray::GEO::SOFT::GPL class object
  my $gpl = $soft->parse;
  # the meta information
  # the platform data is a matrix
  # the names for each column, it is gene id types
  # the names for each row, it is the primary id for rows
  # e.g. probe IDs
  # 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]);


A Platform record is composed of a summary description of the array or sequencer and, for array-based Platforms, a data table defining the array template.Each Platform record is assigned a unique and stable GEO accession number (GPLxxx). A Platform may reference many Samples that have been submitted by multiple submitters. (Copyed from GEO web site).

This module is a simple tool to parse and store platform data. We only extract the most compact meta information and the id matrix for id mapping. Platform data is downloaded from ftp://ftp.ncbi.nih.gov/pub/geo/DATA/annotation/platforms/GPLxxx.annot.gz. This module will not be used directly but always be invoked by Microarray::GEO::SOFT module.


new("file" => $file, "verbose" = 1)>

Initial a GPL class object. The file argument is the platform data in SOFT format or a file handle that has been openned. 'verbose' determines whether print the message when analysis. 'sample_value_column' is the column name for table data when parsing GSM data. The argument is optional and the platform can be download through Microarray::GEO::SOFT.


Retrieve platform information. This soubroutine extracts the basic meta information and a table with different ID types.


Get meta information


Set meta information. Valid argumetns are 'accession', 'title' and 'platform'.


Get table information


Set table information. Valid argumetns are 'rownames', 'colnames' and 'matrix'.


Accession number for the platform


Title of the platform record


Accession number for the platform


primary ID for probes in the platform


Different ID types provided in the platform data


ID type matrix, each column refers to one ID type


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.



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