screen_for_duplicate_markers: Screen for and remove duplicated markers

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description

screen_for_duplicate_markers identifies and merges duplicate markers.

Usage

screen_for_duplicate_markers(dosage_matrix, merge_NA = TRUE,
  plot_cluster_size = TRUE, log = NULL)

Arguments

dosage_matrix	An integer matrix with markers in rows and individuals in columns.
merge_NA	Logical. Should missing values be imputed if non-NA in duplicated marker? By default, TRUE. If FALSE the dosage scores of representing marker are represented in the filtered_dosage_matrix.
plot_cluster_size	Logical. Should an informative plot about duplicate cluster size be given? By default, TRUE.
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

A list containing:

• bin_list list of binned markers. The list names are the representing markers. This information can later be used to enrich the map with binned markers.

• filtered_dosage_matrix dosage_matrix with merged duplicated markers. The markers will be given the name of the marker with least missing values.

Examples

data("screened_data3")
dupmscreened <- screen_for_duplicate_markers(screened_data3)

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