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course 4.0.2.1

Level: intermediate
4.0.2.1 | intermediate | 1 sessions
A lightning presentation on CPAN modules that help you handle spans and sets. This is of interest to those of you who work with objects with spatial coordinates (clones, contigs, alignments, etc) or objects identified by an index set (array probes, ordered features, etc). Focus will be on demonstrating how to use the Set::IntSpan module to calculate coverage and coverage gaps and to find runs in probe sets. Other CPAN modules that implement sets and multisets will be mentioned.

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categories

0 | introduction and orientation

1 | perl fundamentals

2 | shell and prompt tools

3 | web development

4 | CPAN Modules

5 | Ruby

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level: beginner beginner ( 1 )

level: intermediate intermediate ( 2 )

level: advanced advanced ( 3 )

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4.0.2.1 Spans and Sets

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This lecture is targeted for those who work with mapped elements, such as clones, contigs, alignments, array probes, and genomic features. Commonly, these objects need to be manipulated to calculate their overlaps, distances, and coverage. CPAN offers a large number of modules that help you in this regard, specifically Set::IntSpan, Set::IntRange and Set::Window. We'll introduce the Set::IntSpan API and show how it can be used to interrogate two data sets: a collection of clones mapped by end alignments and a set of SNP array results.


Manipulating elements, indexed or with spatial mappings, is made easier with Set::IntSpan.

other in this category

4.1.2.2 | Random Numbers and Distributions

other by same level

2.2.2.2 | Prompt Tools

1.1.2.8 | Intermediate Perl

2.1.2.4 | Data Mining and Analysis at the Command Line

1.2.2.1 | Effective use of map, sort and grep in Perl

4.1.2.2 | Random Numbers and Distributions

other by same instructor

Other courses by Martin Krzywinski.

0.0.0.1 | Orientation Session

0.1.0.1 | Two Problems

2.2.2.2 | Prompt Tools

1.0.1.8 | Introduction to Perl

1.1.2.8 | Intermediate Perl

2.1.2.4 | Data Mining and Analysis at the Command Line

1.2.2.1 | Effective use of map, sort and grep in Perl

4.1.2.2 | Random Numbers and Distributions