NAME

Microarray::GEO::SOFT::GSM - GEO sample data class

SYNOPSIS

  use Microarray::GEO::SOFT:
  my $soft = Microarray::GEO::SOFT->new;
  $soft->download("GSE35505");
  
  my $gse = $soft->parse;
  my $gsm = $gse->list("GSM")->[0];
  
  # the meta information
  $gsm->meta;
  $gsm->platform;
  $gsm->title;
  $gsm->accession;
  
  # the sample data is a matrix (in fact it is a vector)
  $gsm->matrix;
  # the names for each column
  $gsm->colnames;
  $ the names for each row, it is the primary id for rows
  $gsm->rownames;

DESCRIPTION

A Sample record describes the conditions under which an individual Sample was handled, the manipulations it underwent, and the abundance measurement of each element derived from it. Each Sample record is assigned a unique and stable GEO accession number (GSMxxx). A Sample entity must reference only one Platform and may be included in multiple Series. (Copyed from GEO web site).

This module retrieves sample information from series data.

Subroutines

new("file" => $file, "verbose" = 1, 'sample_value_column' => 'VALUE')>

Initial a GSM class object. The first argument is the path of the sample 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.

$gsm->parse

Retrieve sample information. The sample data in SOFT format is alawys a table

$gsm->meta

Get meta information

$gsm->set_meta(HASH)

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

$gsm->table

Get table information

$gsm->set_table

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

$gsm->platform

Accession number for the platform the sample belong to.

$gsm->title

Title of the series record

$gsm->accession

Accession number for the sample

$gsm->rownames

primary ID for probes

$gsm->colnames

['VALUE']

$gsm->matrix

expression value matrix. It is a one column matrix here.

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