screen_for_duplicate_individuals: Screen for duplicate individuals

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description

screen_for_duplicate_individuals identifies and merges duplicate individuals.

Usage

screen_for_duplicate_individuals(dosage_matrix, cutoff = NULL, plot_cor = T,
  log = NULL)

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.

Value

A matrix similar to dosage_matrix, with merged duplicate individuals.

Examples

data("segregating_data")
dupscreened<-screen_for_duplicate_individuals(dosage_matrix=segregating_data,
                                               cutoff=0.9,
                                               plot_cor=TRUE)
## Not run: 
#user input:
data("segregating_data")
screen_for_duplicate_individuals(dosage_matrix=segregating_data, plot_cor=TRUE)

## End(Not run)

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