microbov
(Package: adegenet) :
Microsatellites genotypes of 15 cattle breeds
This data set gives the genotypes of 704 cattle individuals for 30 microsatellites recommended by the FAO. The individuals are divided into two countries (Afric, France), two species (Bos taurus, Bos indicus) and 15 breeds. Individuals were chosen in order to avoid pseudoreplication according to their exact genealogy.
● Data Source:
CranContrib
● Keywords: datasets
● Alias: microbov
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sim2pop
(Package: adegenet) :
Simulated genotypes of two georeferenced populations
This simple data set was obtained by sampling two populations evolving in a island model, simulated using Easypop (2.0.1). See source for simulation details. Sample sizes were respectively 100 and 30 genotypes. The genotypes were given spatial coordinates so that both populations were spatially differentiated.
● Data Source:
CranContrib
● Keywords: datasets
● Alias: sim2pop
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rupica
(Package: adegenet) :
Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the
This data set contains the genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains, in France. No prior clustering about individuals is known. Each genotype is georeferenced. These data also contain a raster map of elevation of the sampling area.
● Data Source:
CranContrib
● Keywords: datasets
● Alias: rupica
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spcaIllus
(Package: adegenet) :
Simulated data illustrating the sPCA
Datasets illustrating the spatial Principal Component Analysis (Jombart et al. 2009). These data were simulated using various models using Easypop (2.0.1). Spatial coordinates were defined so that different spatial patterns existed in the data. The spca-illus is a list containing the following genind or genpop objects:
- dat2A: 2 patches
- dat2B: cline between two pop
- dat2C: repulsion among individuals from the same gene pool
- dat3: cline and repulsion
- dat4: patches and local alternance
● Data Source:
CranContrib
● Keywords: datasets, spatial
● Alias: spcaIllus
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dapcIllus
(Package: adegenet) :
Simulated data illustrating the DAPC
Datasets illustrating the Discriminant Analysis of Principal Components (DAPC, Jombart et al. submitted).
● Data Source:
CranContrib
● Keywords: datasets
● Alias: dapcIllus
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nancycats
(Package: adegenet) :
Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)
This data set gives the genotypes of 237 cats (Felis catus L.) for 9 microsatellites markers. The individuals are divided into 17 colonies whose spatial coordinates are also provided.
● Data Source:
CranContrib
● Keywords: datasets
● Alias: nancycats
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eHGDP
(Package: adegenet) :
Extended HGDP-CEPH dataset
This dataset consists of 1350 individuals from native Human populations distributed worldwide typed at 678 microsatellite loci. The original HGDP-CEPH panel [1-3] has been extended by several native American populations [4]. This dataset was used to illustrate the Discriminant Analysis of Principal Components (DAPC, [5]).
● Data Source:
CranContrib
● Keywords: datasets
● Alias: eHGDP
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H3N2
(Package: adegenet) :
Seasonal influenza (H3N2) HA segment data
The dataset H3N2 consists of 1903 strains of seasonal influenza (H3N2) distributed worldwide, and typed at 125 SNPs located in the hemagglutinin (HA) segment. It is stored as an R object with class genind and can be accessed as usual using data(H3N2) (see example). These data were gathered from DNA sequences available from Genbank (http://www.ncbi.nlm.nih.gov/Genbank/).
● Data Source:
CranContrib
● Keywords: datasets
● Alias: H3N2, USflu, USflu.fasta
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