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.