screen_for_duplicate_markers {polymapR}

Screen for and remove duplicated markers

Description

screen_for_duplicate_markers identifies and merges duplicate markers.

Usage

screen_for_duplicate_markers(
  dosage_matrix,
  merge_NA = TRUE,
  plot_cluster_size = TRUE,
  ploidy,
  ploidy2 = NULL,
  LG_number,
  estimate_bin_size = FALSE,
  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.

ploidy

Ploidy level of parent 1. Only needed if estimate_bin_size is TRUE

ploidy2

Integer, by default NULL. If parental ploidies differ, use this to specify the ploidy of parent 2. Only needed if estimate_bin_size is TRUE

LG_number

Expected number of chromosomes (linkage groups). Only needed if estimate_bin_size is TRUE

estimate_bin_size

Logical, by default FALSE. If TRUE, a very rudimentary calculation is made to estimate the average size of a marker bin, assuming a uniform distribution of cross-over events and on average one cross-over per bivalent.

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)