find_proxmarkers: Find the position of markers near a locus

In neyhartj/qgsim: Simulations of Plant Breeding Experiments

Find the position of markers near a locus

Description

Finds the position of markers near a particular locus. By default, the function returns the flanking markers, however markers within a certain range can also be returned.

Usage

find_proxmarkers(genome, marker, ..., include.qtl = FALSE)

Arguments

genome	An object of class genome.
marker	See find.markerpos.
...	Additional arguments. Markers within a position range of marker can be specified using the min.dist (returns markers at min.dist from marker) and max.dist (returns markers no more than min.dist from marker).
include.qtl	Logical. Should QTL be included in the results? If FALSE, the genome should have a genetic model.
ignore.gen.model	Logical - should the gene model be ignored?

Examples

# Simulate the genome
n.mar  <- c(505, 505, 505)
len <- c(120, 130, 140)

genome <- sim_genome(len, n.mar)

# Sample marker names to lookup
sample_markers <- sample(markernames(genome, include.qtl = TRUE), size = 3)

find_proxmarkers(genome = genome, marker = sample_markers, include.qtl = TRUE)

neyhartj/qgsim documentation built on Nov. 11, 2023, 4:08 p.m.