adegenet 1.3-1: new tools for the analysis of genome-wide SNP data - PubMed (original) (raw)
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data
Thibaut Jombart et al. Bioinformatics. 2011.
Abstract
Summary: While the R software is becoming a standard for the analysis of genetic data, classical population genetics tools are being challenged by the increasing availability of genomic sequences. Dedicated tools are needed for harnessing the large amount of information generated by next-generation sequencing technologies. We introduce new tools implemented in the adegenet 1.3-1 package for handling and analyzing genome-wide single nucleotide polymorphism (SNP) data. Using a bit-level coding scheme for SNP data and parallelized computation, adegenet enables the analysis of large genome-wide SNPs datasets using standard personal computers.
Availability: adegenet 1.3-1 is available from CRAN: http://cran.r-project.org/web/packages/adegenet/. Information and support including a dedicated forum of discussion can be found on the adegenet website: http://adegenet.r-forge.r-project.org/. adegenet is released with a manual and four tutorials totalling over 300 pages of documentation, and distributed under the GNU General Public Licence (≥2).
Contact: t.jombart@imperial.ac.uk.
Supplementary information: Supplementary data are available at Bioinformatics online.
Figures
Fig. 1.
DAPC of simulated data (see text). (a) Density of individual scores on the first discriminant function, with groups represented in red and blue. (b) SNP contribution to the separation of the groups; the last (structured) 1000 SNPs are coloured in green; the last 4000 SNPs are represented in the main plot, while the figure corresponding to all SNPs is shown in inset.
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