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Estimate Genetic Map Positions

Source: R/estimate_map.R
estimate_map.Rd

Calculates genetic map positions for a single chromosome using recombination frequency (RF) and LOD scores from a genotype matrix. The output is standardized for compatibility with Marey plots.

Usage

estimate_map(geno_matrix, model = "Kosambi", n_point = 20, pop.type = "F2")

Arguments

geno_matrix

A genotype matrix (markers as rows, individuals as columns) for one chromosome or linkage group.

model

Character. Mapping function to use: "Kosambi" (default) or "Haldane".

n_point

Integer. The n.point value for interpolation when estimating genetic positions. Default is 20.

pop.type

Character. Population type: "DH", "BC", "F2" (default), "S1", "RIL.self", "RIL.sib".

Value

A data frame with columns:

  • chrom: Chromosome identifier

  • position_Mb: Physical position in megabases

  • position_cM: Genetic distance in centimorgans (estimated)

Details

This function uses MapRtools::MLEL() and MapRtools::genetic_map() for estimating genetic positions. The output is ready to be used with plot_marey().

Examples

if (FALSE) { # \dontrun{
map_chr1 <- estimate_map(geno_matrix = chr1_geno_matrix, n_point = 20)
plot_marey(map_chr1, chrom = "CHR1")
} # }