example_corr: Example local ancestry correlation

In kegrinde/STEAM: Significance Threshold Estimation for Admixture Mapping

Example local ancestry correlation

Description

Data frame containing local ancestry correlation at pairs of loci separated by various distances apart, for an admixed population with 2 ancestral populations, 6 generations since admixture, and admixture proportions contained in example_props. Values generated by adding noise to expected correlation, and some values may lie outside (-1,1), which in practice should not occur.

Format

Data frame should 3 columns named theta, corr, and anc. The theta column contains recombination fraction between loci. The corr column contains correlation in local ancestry at the loci. The anc column indicated which ancestral components are being compared (e.g., '1_1', '1_2'). Number of rows does not matter.

Source

Toy example generated with command thetas <- seq(0, 0.5, length = 51); corr_K2_11 <- sapply(thetas, function(x) exp_corr(x, g = 6, props = example_props, k1 = 1, k2 = 1)); corr_K2_12 <- sapply(thetas, function(x) exp_corr(x, g = 6, props = example_props, k1 = 1, k2 = 2)); corr_K2_22 <- sapply(thetas, function(x) exp_corr(x, g = 6, props = example_props, k1 = 2, k2 = 2)); set.seed(1); example_corr <- data.frame(theta = rep(thetas, times = 3),corr = c(corr_K2_11, corr_K2_12, corr_K2_22) + rnorm(n = length(thetas)*3, mean = 0, sd = 0.01), anc = rep(c('1_1', '1_2', '2_2'), each = length(thetas)))

kegrinde/STEAM documentation built on June 30, 2024, 11:27 p.m.