Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.
CONCLUSIONS
Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware.


METHODS
Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at (http://www.bioconductor.org).
Carey
Vincent J
VJ
Channing Laboratory, Department of Medicine, I2B2 National Center for Biocomputing, Brigham and Women's Hospital, Boston, MA 02115, USA. stvjc@channing.harvard.edu
Davis
Adam R
AR
Lawrence
Michael F
MF
Gentleman
Robert
R
Raby
Benjamin A
BA
D000465:Algorithms; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D005838:Genotype; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software