popkin (version 1.2.2)

inbr: Extract inbreeding coefficients from a kinship matrix

Description

The kinship matrix contains inbreeding coefficients \(f_j^T\) along the diagonal, present as \(\phi_{jj}^T = \frac{1}{2}(1+f_j^T)\). This function extracts the vector of \(f_j^T\) values from the input kinship matrix.

Usage

inbr(kinship)

Arguments

kinship

The \(n \times n\) kinship matrix.

Value

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

Examples

# NOT RUN {
#########
# 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)

# }