Shared Loci

Description

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

Usage

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propSharedLoci(g, type = c("strata", "ids"), num.cores = NULL)

sharedAlleles(g, smry = c("num", "which"))

propSharedIds(ids, g, id.row.mat = idRows(g)[ids, ])

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.

id.row.mat

lookup matrix of id row names or numbers of a format like the one generated by idRows.

Value

data.frame summary of pairwise shared loci.

Author(s)

Eric Archer eric.archer@noaa.gov

Examples

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data(msats.g)
msats.g <- stratify(msats.g, "fine")

sharedAlleles(msats.g)

## Not run: 
propSharedLoci(msats.g, num.cores = 2)

## End(Not run)

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