[Bioc-devel] Course: Understanding R / Bioconductor, Sept 30-Oct 1, Seattle

Martin Morgan mtmorgan at fhcrc.org
Mon Aug 26 01:40:57 CEST 2013

Bioconductors --

Please join us for an intermediate course on Understanding R / Bioconductor, to 
be held in Seattle on Sept 30 / Oct 1.


This intermediate course is directed at R / Bioconductor users who, in an effort 
to get the most out of high-throughput sequence and other analyses, want to 
understand more about how R and Bioconductor work. (1) The course begins by 
reviewing R data types, memory management, and other aspects of internal 
computation. We use this as a basis for understanding how to writing, debug, and 
assess the performance of efficient R code, including straight-forward 
approaches to iteration, vectorization, and parallel evaluation. (2) We then 
explore R objects, especially the S4 object system. We learn about how to 
specify simple and more complicated S4 objects, and how to implement essential 
methods for single and multiple dispatch. We use insights from performance and 
the S4 class system to explore strategies for efficient representation of large 
structured data, especially the classes in the IRanges, GenomicRanges, 
VariantAnnotation, and Biostrings packages. (3) Availability of programming 
libraries (such as samtools) or performance needs may sometimes point to use of 
C or C++ code integrated into R. We develop some simple C functions, and explore 
use of Rcpp as a relatively painless way to incorporate C code. We take a brief 
look at R's internal data representations, and explore how to debug and profile 
C code. (4) Finally, we investigate how R can be used to interact with other 
important resources: data bases; web sites; and visualization facilities like 
shiny. Use of some of these facilities is illustrated by packages such as 
AnnotationDbi and biomaRt.

Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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