n_eff: Calculates the effective sample size of the data

In popkin: Estimate Kinship and FST under Arbitrary Population Structure

Calculates the effective sample size of the data

Description

The effective sample size n_eff is the equivalent number of independent haplotypes that gives the same variance as that observed under the given population. The variance in question is for the weighted sample mean ancestral allele frequency estimator. It follows that n_eff equals the inverse of the weighted mean kinship. If max = TRUE, a calculation is performed that implicitly uses optimal weights which maximize n_eff, which equals the sum of the elements of the inverse kinship matrix. However, if nonneg = TRUE and if the above solution has negative weights (common), optimal non-negative weights are found instead (there are three algorithms available, see algo). If max = FALSE, then the input weights are used in this calculation, and if weights are NULL, uniform weights are used.

Usage

n_eff(
  kinship,
  max = TRUE,
  weights = NULL,
  nonneg = TRUE,
  algo = c("gradient", "newton", "heuristic"),
  tol = 1e-10
)

Arguments

kinship	An n-by-n kinship matrix.
max	If TRUE, returns the maximum n_eff value among those computed using all possible vectors of weights that sum to one (and which are additionally non-negative if nonneg = TRUE). If FALSE, n_eff is computed using the specific weight vector provided.
weights	Weights for individuals (optional). If NULL, uniform weights are used. This parameter is ignored if max = TRUE.
nonneg	If TRUE (default) and max = TRUE, non-negative weights that maximize n_eff are found. See algo. This has no effect if max = FALSE.
algo	Algorithm for finding optimal non-negative weights (applicable only if nonneg = TRUE and max = TRUE and the weights found by matrix inversion are non-negative). May be abbreviated. If "gradient" (default), an optimized gradient descent algorithm is used (fastest; recommended). If "newton", the exact multivariate newton's Method is used (slowest since (n+1)-by-(n+1) Hessian matrix needs to be inverted at every iteration; use if possible to confirm that "gradient" gives the best answer). If "heuristic", if the optimal solution by the inverse matrix method contains negative weights, the most negative weight in an iteration is forced to be zero in all subsequent iterations and the rest of the weights are solved for using the inverse matrix method, repeating until all resulting weights are non-negative (also slow, since inversion of large matrices is required; least likely to find optimal solution).
tol	Tolerance parameter for "gradient" and "newton" algorithms. The algorithms converge when the norm of the step vector is smaller than this tolerance value.

Details

The maximum n_eff possible is 2 * n, where n is the number of individuals; this value is attained only when all haplotypes are independent (a completely unstructured population in Hardy-Weinberg equilibrium). The minimum n_eff possible is 1, which is attained in an extremely structured population with FST of 1, where every individual has exactly the same haplotype at every locus (no heterozygotes). Moreover, for K extremely-differentiated subpopulations (FST = 1 per subpopulation) n_eff = K. In this way, n_eff is smaller than the ideal value of 2 * n depending on the amount of kinship (covariance) in the data.

Occasionally, depending on the quality of the input kinship matrix, the estimated n_eff may be outside the theoretical [1, 2*n] range, in which case the return value is set to the closest boundary value. The quality of the results depends on the success of matrix inversion (which for numerical reasons may incorrectly contain negative eigenvalues, for example) or of the gradient optimization.

Value

A list containing n_eff and weights (optimal weights if max = TRUE, input weights otherwise).

Examples

# Get n_eff from a genotype matrix

# 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 "kinship" from the genotypes "X"!
kinship <- popkin(X, subpops) # calculate kinship from X and optional subpop labels
weights <- weights_subpops(subpops) # can weigh individuals so subpopulations are balanced

# use kinship matrix to calculate n_eff
# default mode returns maximum n_eff possible across all non-negative weights that sum to one
# also returns the weights that were optimal
obj <- n_eff(kinship)
n_eff_max <- obj$n_eff
w_max <- obj$weights

# version that uses weights provided
obj <- n_eff(kinship, max = FALSE, weights = weights)
n_eff_w <- obj$n_eff
w <- obj$weights # returns input weights renormalized for good measure

# no (or NULL) weights implies uniform weights
obj <- n_eff(kinship, max = FALSE)
n_eff_u <- obj$n_eff
w <- obj$weights # uniform weights

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