LD_computation: LD_computation

In vincentgarin/mppSim: Functions for simulation in MPP

LD_computation

Description

Calculate linkage disequilibrium (LD) between a set of markers

Usage

LD_computation(
  geno,
  map,
  pop_ind = NULL,
  max_g_dist = 30,
  chr_sel = 1,
  prop_mk_comb = 1
)

Arguments

geno	Numeric genotype marker matrix coded in 0, 1, 2 representing the number of allele copies of one allele (e.g. second parent, minor allele). Genotypes in row and markers in column. The column (marker) name should be identical to the first column of the map (marker indicators). Can be obtrained with sim_mpp_cross
map	data.frame representing the marker map information with the following columns: 1) character marker identifier; 2) numeric chromosomes (1, 2, 3, ...); 3) numeric genetic distance in cM; 4) numeric Optional physical distance in bp.
pop_ind	Optional population indicator Character vector indicating to which (sup)population each genotype belongs. Default = NULL
max_g_dist	Numeric value between 0 and 1 indicating the proportion of marker pairs selected to calculate the LD. Default = 1

Value

data.frame with marker i and j position, genetic distance (physical distance) beteen markers and LD

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)

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