strataG (version 2.0.2)

sharedLoci: Shared Loci

Description

Calculate proportion of alleles and number of loci shared between pairs of individuals or strata.

Usage

propSharedLoci(g, type = c("strata", "ids"), num.cores = NULL)
sharedAlleles(g, smry = c("num", "which"))
.propSharedIds(ids, gt)

Arguments

g

a '>gtypes object.

type

a character vector determining type of pairwise comparsion. Can be "strata" for strata or "ids" for individuals.

num.cores

number of CPU cores to use. Defaults to the number reported by detectCores - 1.

smry

a character vector determining type of summary for sharedAlleles. "which" returns the names of the alleles shared. "num" returns the number of alleles shared.

ids

character vector of two sample ids to compare.

gt

array of genotypes generated by as.array.gtypes.

gt

genotypes array resulting from a call to as.array(g)

Value

data.frame summary of pairwise shared loci.

Examples

# NOT RUN {
data(msats.g)
msats.g <- stratify(msats.g, "fine")

sharedAlleles(msats.g)

# }
# NOT RUN {
propSharedLoci(msats.g, num.cores = 2)
# }
# NOT RUN {
# }