R: The Eurasian subset of the HGDP dataset used in example...
HGDP.bedassle.data
R Documentation
The Eurasian subset of the HGDP dataset used in example BEDASSLE analyses
Description
The allelic counts, sample sizes, geographic distances, ecological distances, and
population metadata from the 38 human populations used in example BEDASSLE
analyses, subsetted from the Human Genome Diversity Panel (HGDP) dataset.
A matrix of allelic count data, for which nrow =
the number of populations and ncol = the number of bi-allelic loci
sampled. Each cell gives the number of times allele ‘1’ is observed in each
population. The choice of which allele is allele ‘1’ is arbitrary, but must
be consistent across all populations at a locus.
sample.sizes
A matrix of sample sizes, for which nrow = the number
of populations and ncol = the number of bi-allelic loci sampled
(i.e. - the dimensions of sample.sizes must match those of
counts). Each cell gives the number of chromosomes successfully
genotyped at each locus in each population.
Geo.Distance
Pairwise geographic distance (D_{i,j}). This may be
Euclidean, or, if the geographic scale of sampling merits it, great-circle
distance. In the case of this dataset, it is great-circle distance.
Eco.Distance
Pairwise ecological distance(s) (E_{i,j}), which may
be continuous (e.g. - difference in elevation) or binary (same or opposite
side of some hypothesized barrier to gene flow). In this case, the
ecological distance is binary, representing whether a pair of populations
occurs on the same side, or on opposite sides, of the Himalayas.
number.of.populations
The number of populations in the analysis.
This should be equal to nrow(counts). In this dataset, there
are 38 populations sampled.
number.of.loci
The number of loci in the analysis. This should be equal
to ncol(counts). In this dataset, there are 1000 loci
sampled.
hgdp.metadata
This data frame contains the metadata on the populations
included in the analysis, including:
Population name
Latitude
Longitude
Source
Conrad et al. A worldwide survey of haplotype variation and linkage
disequilibrium in the human genome. Nature Genetics 2008.
Li et al. Worldwide human relationships inferred from genome-wide
patterns of variation. Science 2008.
References
Bradburd, G.S., Ralph, P.L., and Coop, G.M. Disentangling the effects of
geographic and ecological isolation on genetic differentiation.
Evolution 2013.
Examples
## see command{MCMC}, command{MCMC_BB}, command{calculate.pariwise.Fst},
## command{calculate.all.pairwise.Fst}, and command{Covariance} for usage.