/ 
bioperl-microarray-0.1
/ Bio::Expression::MicroarrayIO

NAME

Bio::Expression::MicroarrayIO - Read/write Microarray files

SYNOPSIS

  use Bio::Expression::MicroarrayIO;

  $stream  = Bio::Expression::MicroarrayIO->new(
		'-file'     => "my.cel",
		'-template' => "my.cdf",
		'-format'   => "affymetrix",
						);

  while ( my $in = $stream->next_array() ) {
    print $in->id() . "\n";
  }

DESCRIPTION

The Bio::Expression::MicroarrayIO module reads various Microarray data formats such as Affymetrix CEL and CDF, and dChip XLS.

CONSTRUCTORS

Bio::Expression::MicroarrayIO->new()

   $str = Bio::Expression::MicroarrayIO->new(
		-file     => 'filename',
		-template => 'template',
		-format   =>  $format
											);

The new() class method constructs a new Bio::Expression::MicroarrayIO object. The returned object can be used to retrieve or print cluster objects. new() accepts the following parameters:

-file

A file path to be opened for reading.

-format

Specify the format of the file. Supported formats include:

affymetrix		*.cel	Affymetrix CEL files

The format name is case insensitive. 'AFFYMETRIX', 'Affymetrix' and 'affymetrix' are all supported.

-template

Affymetrix CEL, and other microarray files, require a template file that defines the location of probes on the array. This template is necessary to match values from a matrix of values from a data file with sets of probes that are on the array. Pass the path to the template file as the -template parameter.

OBJECT METHODS

See below for more detailed summaries. The main methods are:

$array = $str->next_array()

Fetch the next array from the stream.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/MailList.shtml      - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

AUTHOR - Allen Day

Email allenday@ucla.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : Bio::Expression::MicroarrayIO->new(
		-file     => 'path/to/filename',
		-format   => 'format',
		-template => 'path/to/template');
 Function: Returns a new microarray stream
 Returns : A Bio::Expression::MicroarrayIO handler.
 Args    : -file     => filename
           -format   => format
           -template => template

_initialize

Title   : _initialize
Usage   : $stream->_initialize(@args);
Function: Initialize the object's IO handles
Returns :
Args    : @_ from new()

next_array

Title   : next_array
Usage   : $ary = $stream->next_array()
Function: Reads the next array object from the stream and returns it.
Returns : a (hopefully) Bio::Expression::MicroarrayI compliant object
Args    : none

_load_format_module

Title   : _load_format_module
Usage   : $stream->_load_format_module($format)
Function: Loads a module for $format at run time
Returns : 1 on success, undef on failure
Args    : the name of a microarray format (class name)

_guess_format

Title   : _guess_format
Usage   : $stream->_guess_format($filename)
Function: guess format based on file suffix
Example :
Returns : guessed format of filename (lower case)
Args    : filename