polymapR (version 1.1.1)

screen_for_duplicate_individuals: Screen for duplicate individuals

Description

screen_for_duplicate_individuals identifies and merges duplicate individuals.

Usage

screen_for_duplicate_individuals(
  dosage_matrix,
  cutoff = NULL,
  plot_cor = T,
  log = NULL,
  saveCOV = "PearsonCC"
)

Arguments

dosage_matrix

An integer matrix with markers in rows and individuals in columns.

cutoff

Correlation coefficient cut off. At this correlation coefficient, individuals are merged. If NULL user input will be asked after plotting.

plot_cor

Logical. Should correlation coefficients be plotted? Can be memory/CPU intensive with high number of individuals.

log

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

saveCOV

= "PearsonCC"

Value

A matrix similar to dosage_matrix, with merged duplicate individuals.

Examples

# NOT RUN {
#user input:
data("segregating_data")
screen_for_duplicate_individuals(dosage_matrix=segregating_data,cutoff=0.9,plot_cor=TRUE)
# }