NAME

Bio::ToolBox::db_helper::bigbed

DESCRIPTION

This module provides support for binary BigBed files to the Bio::ToolBox package.

USAGE

The module requires Bio::DB::BigBed to be installed, which in turn requires the UCSC Kent C library to be installed.

In general, this module should not be used directly. Use the methods available in Bio::ToolBox::db_helper or <Bio::ToolBox::Data>.

All subroutines are exported by default.

Available subroutines

collect_bigbed_scores

This subroutine will collect only the data values from a binary bigbed file for the specified database region. The positional information of the scores is not retained.

The subroutine is passed a parameter array reference. See below for details.

The subroutine returns an array or array reference of the requested dataset values found within the region of interest.

collect_bigbed_position_scores

This subroutine will collect the score values from a binary bigBed file for the specified database region keyed by position.

The subroutine is passed a parameter array reference. See below for details.

The subroutine returns a hash of the defined dataset values found within the region of interest keyed by position. The feature midpoint is used as the key position. When multiple features are found at the same position, a simple mean (for score or length data methods) or sum (for count methods) is returned.

open_bigbed_db()

This subroutine will open a BigBed database connection. Pass either the local path to a bigBed file (.bb extension) or the URL of a remote bigBed file. It will return the opened database object.

The opened BigBed object is cached for later use. If you do not want this (for example, when forking), pass a second true argument.

sum_total_bigbed_features()

This subroutine will sum the total number of bed features present in a BigBed file. This may be useful, for example, in calculating fragments (reads) per million mapped values when the bigbed file represents sequence alignments.

Pass either the name of a bigBed file (.bb), either local or remote, or an opened BigBed database object. A scalar value of the total number of features is returned.

Data Collection Parameters Reference

The data collection subroutines are passed an array reference of parameters. The recommended method for data collection is to use get_segment_score() method from Bio::ToolBox::db_helper.

The parameters array reference includes these items:

1. The chromosome or seq_id

1. The start position of the segment to collect

3. The stop or end position of the segment to collect

4. The strand of the segment to collect

Should be standard BioPerl representation: -1, 0, or 1.

5. The strandedness of the data to collect

A scalar value representing the desired strandedness of the data to be collected. Acceptable values include "sense", "antisense", or "all". Only those scores which match the indicated strandedness are collected.

6. The method for combining scores.

Acceptable values include score, count, and pcount.

   * score returns the basepair coverage of alignments over the 
   region of interest
   
   * count returns the number of alignments that overlap the 
   search region. 
   
   * pcount, or precise count, returns the count of alignments 
   whose start and end fall within the region. 
   
   * ncount, or named count, returns an array of alignment read  
   names. Use this to avoid double-counting paired-end reads by 
   counting only unique names. Reads are taken if they overlap 
   the search region.
   

7. A database object.

Not used here.

8 and higher. Paths to one or more BigBed files

Opened BigBed file objects are cached. Both local and remote files are supported.

AUTHOR

 Timothy J. Parnell, PhD
 Howard Hughes Medical Institute
 Dept of Oncological Sciences
 Huntsman Cancer Institute
 University of Utah
 Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.