af_snp: Allele frequencies for SNP

In StoreyLab/lfa: Logistic Factor Analysis for Categorical Data

Allele frequencies for SNP

Description

Computes individual-specific allele frequencies for a single SNP.

Usage

af_snp(snp, LF, max_iter = 100, tol = 1e-10)

Arguments

snp	vector of 0's, 1's, and 2's
LF	Matrix of logistic factors, with intercept. Pass in the return value from lfa()!
max_iter	Maximum number of iterations for logistic regression
tol	Numerical tolerance for convergence of logistic regression

Value

vector of allele frequencies

See Also

af()

Examples

LF <- lfa(hgdp_subset, 4)
# pick one SNP only
snp <- hgdp_subset[ 1, ]
# allele frequency vector for that SNO only
allele_freqs_snp <- af_snp(snp, LF)

StoreyLab/lfa documentation built on June 10, 2025, 9:34 a.m.