polymapR (version 1.0.17)

marker_binning_list: Bin markers that are in a nested list

Description

This is a wrapper for marker_binning. It applies marker_binning to a nested list as output of split_linkage_info

Usage

marker_binning_list(dosage_matrix, linkage_list, r_thresh = NA,
  lod_thresh = NA, return_removed_marker_info = FALSE, log = NULL, ...)

Arguments

dosage_matrix

A dosage matrix

linkage_list

A nested list with linkage group on the first level and homologue on the second.

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.

return_removed_marker_info

Logical. Should removed marker information be returned? If TRUE, output is a list containing the linkage list with binned markers removed and a dataframe with removed marker information.

log

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

…

Arguments passed to marker_binning

Value

A list of linkage data.frames with binned markers removed. If return_removed_marker_info = TRUE, a list containing the above linkage dataframes (linkage_list) and a dataframe with removed marker information, called removed_markers.

Examples

# NOT RUN {
data("screened_data3", "all_linkages_list_P1_split")
mb<-marker_binning_list(screened_data3,
                     all_linkages_list_P1_split,
                     target_parent="P1",
                     other_parent="P2")
# }