View source: R/exported_functions.R
screen_for_duplicate_markers | R Documentation |
screen_for_duplicate_markers
identifies and merges duplicate markers.
screen_for_duplicate_markers(
dosage_matrix,
merge_NA = TRUE,
plot_cluster_size = TRUE,
ploidy,
ploidy2 = NULL,
LG_number,
estimate_bin_size = FALSE,
log = NULL
)
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, |
plot_cluster_size |
Logical. Should an informative plot about duplicate cluster size be given? By default, |
ploidy |
Ploidy level of parent 1. Only needed if |
ploidy2 |
Integer, by default |
LG_number |
Expected number of chromosomes (linkage groups). Only needed if |
estimate_bin_size |
Logical, by default |
log |
Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout. |
A list containing:
list of binned markers. The list names are the representing markers. This information can later be used to enrich the map with binned markers.
dosage_matrix with merged duplicated markers. The markers will be given the name of the marker with least missing values.
data("screened_data3")
dupmscreened <- screen_for_duplicate_markers(screened_data3)
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