https://github.com/jokergoo/microarray-geo-soft

Reading microarray data in SOFT format from GEO database
https://github.com/jokergoo/microarray-geo-soft

Last synced: 23 days ago
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Reading microarray data in SOFT format from GEO database

• Host: GitHub
• URL: https://github.com/jokergoo/microarray-geo-soft
• Owner: jokergoo
• Created: 2012-08-28T12:50:17.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2014-12-24T16:41:54.000Z (almost 10 years ago)
• Last Synced: 2024-10-14T11:11:17.353Z (2 months ago)
• Language: Perl
• Homepage:
• Size: 262 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
## Reading microarray data in SOFT format from GEO database.

### install

```

cpan -i Microarray::GEO::SOFT

```

### usage

```perl

use Microarray::GEO::SOFT;

use strict;

 

# initialize

my $soft = Microarray::GEO::SOFT->new; 

 

# download

$soft->download("GDS3718");

$soft->download("GSE10626");

$soft->download("GPL1261");

 

# or else you can read local data

$soft = Microarray::GEO::SOFT->new(file => "GDS3718.soft");

$soft = Microarray::GEO::SOFT->new(file => "GSE10626_family.soft");

$soft = Microarray::GEO::SOFT->new(file => "GPL1261.annot");

 

# parse

# it returns a  Microarray::GEO::SOFT::GDS,

# Microarray::GEO::SOFT::GSE or Microarray::GEO::SOFT::GPL object

# according the the GSE ID type

my $data = $soft->parse;

 

# some meta info

$data->meta;

$data->title;

$data->platform;

 

# for GPL and GDS, you can get the data table

$data->table;

$data->colnames;

$data->rownames;

$data->matrix;

 

# sinece GSE can contain more than one GPL

# we can get the GPL list in a GSE

my $gpl_list = $data->list("GPL");

 

# merge samples belonging to a same GPL into a data set

my $gds_list = $data->merge;

 

# if the GSE only have one platform

# then the merged data set is the first one in gds_list

# and the platform is the first one in gpl_list

my $g = $gds_list->[0];

my $gpl = $gpl_list->[0];

 

# since GPL data contains different mapping of genes or probes

# we can transform from probe id to gene symbol

# it returns a Microarray::ExprSet object

my $e = $g->id_convert($gpl, "Gene Symbol");

my $e = $g->id_convert($gpl, qr/gene[-_\s]?symbol/i);

 

 

# if you pased a GDS data

# you can first find the platform

my $platform_id = $data->platform;

# downloaded or parse the local file

my $gpl = Microarray::GEO::SOFT->new->download($platform_id);

# and do the id convert thing

my $e = $data->id_convert($gpl, qr/gene[-_\s]?symbol/i);

 

# or just transform into Microarray::ExprSet direct from GDS

my $e = $g->soft2exprset;

 

# then you can do some simple processing thing

# eliminate the blank lines

$e->remove_empty_features;

 

# make all symbols unique

$e->unify_features;

 

# obtain the expression matrix

$e->save('some-file');

```

### command line

```

getgeo --id=GDS3718

getgeo --file=GDS3718.soft --verbose

```

options are

```

--id=[GEOID]

 

  GEO ID. such as GSE123, GDS123 or GPL123. If this is set, the script would

  download data from GEO FTP site.

 

--proxy=[PROXY]

 

  Proxy to connect to GEO FTP site. Format should look like

  http://username:password@host:port/.

 

--file=[FILE]

 

  Filename for local GEO file. If --id is set, this option is ignored.

 

--tmp-dir=[DIR]

 

  Temporary directory name for processing of GEO data. By default it is

  '.tmp_soft' in your working directory.

 

--verbose

 

  Whether print message while processing.

 

--sample-value-column=[FIELD]

 

  Since there may be multiple columns in GSM record, users may specify which

  column is the expression value they want. By default it is 'VALUE'. Ignored

      when analyzing GPL and GDS data.

 

--output-file=[FILE]

 

  Filename for the output file. By default it is 'GEOID.table' in your current

 

  working directory.

 

--help

 

  Help message.

  ```