LD_decay: LD_decay

In vincentgarin/mppSim: Functions for simulation in MPP

LD_decay

Description

Calculate linkage disequilibrium decay

Usage

LD_decay(LD_data, threshold = 0.1)

Arguments

LD_data	data.frame obtained from function LD_computation
threshold	Numerical value of vector of LD thresholds. Default = 0.1

Value

data.frame LD decay limit(s) in genetic distance per LD threshold

Examples

data("geno_par")
rownames(geno_par) <- paste0('P', 1:nrow(geno_par))

data("EUNAM_map")
rownames(map) <- map[, 1]

# NAM crossing scheme with 3 parents
cross_scheme <- cross_scheme_NAM(3)

geno <- sim_mpp_cross(geno_par = geno_par, map = map,
                     cross_scheme = cross_scheme,
                     n_ind_cr = c(100, 100),
                     geno_score_format = "numeric_IBD")

cr_ind <- substr(x = rownames(geno), start = 1, stop = 3)

LD_chr1 <- LD_computation(geno = geno, map = map, pop_ind = cr_ind,
                         max_g_dist = 40, chr_sel = 1, prop_mk_comb = 1)

LD_plot(LD_chr1)

LD_decay_01 <- LD_decay(LD_chr1)

vincentgarin/mppSim documentation built on Oct. 11, 2024, 3:18 p.m.