pwfst: Estimate the individual-level pairwise FST matrix

In popkin: Estimate Kinship and FST under Arbitrary Population Structure

Estimate the individual-level pairwise FST matrix

Description

This function construct the individual-level pairwise FST matrix implied by the input kinship matrix. If the input is the true kinship matrix, the return value corresponds to the true pairwise FST matrix. On the other hand, if the input is the estimated kinship returned by popkin(), the same code results in the return value being the pairwise FST estimates described in our paper. In all cases the diagonal of the pairwise FST matrix is zero by definition.

Usage

pwfst(kinship)

Arguments

kinship

The n-by-n kinship matrix

Value

The n-by-n pairwise FST matrix

Examples

# 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

# lastly, compute pairwise FST matrix from the kinship matrix
pwF <- pwfst(kinship)
 

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