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->field;
$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
This module retrieves sample information from microarray data. The module is used within parsing GSE data.
Subroutines
new("file" = $file)-
Initial a GSM class object. The only argument is the path of the microarray data in SOFT format or a file handle that has been openned.
$gsm->parse-
Retrieve sample information from microarray data. The sample data in SOFT format is alawys a table
$gsm->meta-
Get meta information
$gsm->platform-
Get accession number of the platform
$gsm->title-
Title of the platform record
$gsm->field-
Description of each field in the data matrix
$gsm->accession-
Accession number for the sample
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.