marker_binning {polymapR}

Perform binning of markers.

Description

marker_binning allows for binning of very closely linked markers and choses one representative.

Usage

marker_binning(
  dosage_matrix,
  linkage_df,
  r_thresh = NA,
  lod_thresh = NA,
  target_parent = "P1",
  other_parent = "P2",
  max_marker_nr = NULL,
  max_iter = 10,
  log = NULL
)

Arguments

dosage_matrix

A dosage matrix.

linkage_df

A linkage data.frame.

r_thresh

Numeric. Threshold at which markers are binned. Is calculated if NA.

lod_thresh

Numeric. Threshold at which markers are binned. Is calculated if NA.

target_parent

A character string specifying the name of the target parent.

other_parent

A character string specifying the name of the other parent.

max_marker_nr

The maximum number of markers per homologue. If specified, LOD threshold is optimized based on this number.

max_iter

Maximum number of iterations to find optimum LOD threshold. Only used if max_marker_nr is specified.

log

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

A list with the following components:

binned_df

A linkage data.frame with binned markers removed.

removed

A data.frame containing binned markers and their representatives.

left

Integer. Number markers left.

Examples

data("screened_data3", "all_linkages_list_P1_split")
binned_markers<-marker_binning(screened_data3, all_linkages_list_P1_split[["LG2"]][["homologue3"]])