CRAN

adegenet 2.0.1

Exploratory Analysis of Genetic and Genomic Data

Released Feb 15, 2016 by Thibaut Jombart, Zhian N. Kamvar, Roman Lustrik, Caitlin Collins, Marie- Pauline Beugin, Brian Knaus, Peter Solymos, Klaus Schliep, Ismail Ahmed, Anne Cori, Federico Calboli

This package cannot yet be used with Renjin it depends on other packages which are not available: shiny 0.13.0, igraph 1.0.1, seqinr 3.1-3, and vegan 2.3-3

Dependencies

igraph 1.0.1 vegan 2.3-3 seqinr 3.1-3 shiny 0.13.0 dplyr 0.4.3 MASS 7.3-45 reshape2 1.4.1 spdep 0.5-92 ggplot2 2.0.0 boot 1.3-17 ade4 1.7-3 ape 3.4

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.