marker_binning: Perform binning of markers.

In polymapR: Linkage Analysis in Outcrossing Polyploids

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"]])

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.