inbr: Extract inbreeding coefficients from a kinship matrix

Description Usage Arguments Value Examples

View source: R/inbr.R

Description

The kinship matrix Φ^T contains inbreeding coefficients f_j^T along the diagonal, present as φ_jj^T = (1+f_j^T)/2. This function extracts the vector of f_j^T values from the input Φ^T.

Usage

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inbr(Phi)

Arguments

Phi

The n-by-n kinship matrix Φ^T.

Value

The length-n vector of inbreeding coefficients f_j^T for each individual j.

Examples

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## Construct toy data
X <- matrix(c(0,1,2,1,0,1,1,0,2), nrow=3, byrow=TRUE) # genotype matrix
subpops <- c(1,1,2) # subpopulation assignments for individuals

## NOTE: for BED-formatted input, use BEDMatrix!
## "file" is path to BED file (excluding .bed extension)
# library(BEDMatrix)
# X <- BEDMatrix(file) # load genotype matrix object

## estimate the kinship matrix "Phi" from the genotypes "X"!
Phi <- popkin(X, subpops) # calculate kinship from X and optional subpop labels

## extract inbreeding coefficients from Phi
inbr <- inbr(Phi)

popkin documentation built on Jan. 27, 2018, 1:03 a.m.