inbr: Extract inbreeding coefficients from a kinship matrix

In popkin: Estimate Kinship and FST under Arbitrary Population Structure

Extract inbreeding coefficients from a kinship matrix

Description

The kinship matrix contains transformed inbreeding coefficients along the diagonal. This function extracts the vector of inbreeding values from the input kinship matrix, by transforming the diagonal using the formula 2 * x - 1.

Usage

inbr(kinship)

Arguments

kinship

The n-by-n kinship matrix.

Value

The length-n vector of inbreeding coefficient for each individual.

See Also

inbr_diag() to replace kinship diagonal with inbreeding values (better for plots)

Examples

#########
# illustrate the main transformation on a 2x2 kinship matrix:
# same inbreeding values for both individuals
inbr <- 0.2
# corresponding self kinship (diagonal values) for both individuals
kinship_self <- (1 + inbr)/2
# actual kinship matrix (zero kinship between individuals)
kinship <- matrix(c(kinship_self, 0, 0, kinship_self), nrow=2)
# expected output of inbr (extracts inbreeding coefficients)
inbr_exp <- c(inbr, inbr)
# actual output from this function
inbr_obs <- inbr(kinship)
# verify that they match (up to machine precision)
stopifnot( all( abs(inbr_obs - inbr_exp) < .Machine$double.eps ) )

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

# extract inbreeding coefficients from Kinship
inbr <- inbr(kinship)

popkin documentation built on Jan. 7, 2023, 1:26 a.m.