Trim Linkage Groups Based on LOD Thresholds

trim_LG is an interactive or scripted function that helps the user filter markers within a specified chromosome based on linkage group (LG) assignment using LOD score thresholds. The user can interactively choose LOD thresholds or provide them via arguments, visualize haplotype frequency before and after filtering, and remove outliers.

Usage

trim_LG(
  chromosome,
  map,
  geno,
  pop_type = "F2",
  drop_outliers = TRUE,
  n_cores = NULL,
  interactive = TRUE,
  initial_LOD = NULL,
  end_LOD = NULL,
  step_LOD = NULL,
  selected_thresh = NULL
)

Arguments

chromosome: Character. The chromosome ID to be processed.
map: A data frame with at least columns "marker", "chrom", and "position".
geno: A genotype matrix (rows = markers, columns = individuals). Preferably binned.
pop_type: Character. Population type for LOD estimation. Default is "F2".
drop_outliers: Logical. Whether to remove outliers based on haplotype frequency. Default is TRUE.
n_cores: Integer. Number of cores to use. If NULL, uses maximum available minus one.
interactive: Logical. If TRUE, asks user for LOD thresholds. If FALSE, requires threshold arguments.
initial_LOD: Numeric. Initial LOD value (required if interactive = FALSE).
end_LOD: Numeric. Final LOD value (required if interactive = FALSE).
step_LOD: Numeric. Step size for LOD sequence (required if interactive = FALSE).
selected_thresh: Numeric. Final LOD threshold to use (required if interactive = FALSE).

Value

A list with filtered genotypes, final map, plots, and LOD settings.

Details

Inspired by functions by Professor Jeffrey B. Endelman’s MapRtools.