[BioC] 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.
https://secure.bioconductor.org/UnderstandingRBioc/
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
Bioconductor
--
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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