marker_binning_list: Bin markers that are in a nested list

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

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

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")

mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.