Home of the Bioinformatics Perl Workshop

perl workshop > courses > spans and sets (4.0.2.1)

course 4.0.2.1

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.

course home <

syllabus <

lecture notes <

tools <

legend

course code

cat.course.level.sessions.session

e.g. 1.0.1.8

levels

level: all all ( 0 )

level: beginner beginner ( 1 )

level: intermediate intermediate ( 2 )

level: advanced advanced ( 3 )

[ consider using for instead of foreach ]

4.0.2.1 Spans and Sets

course home

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.