PCA_progeny: Perform a PCA on progeny

In polymapR: Linkage Analysis in Outcrossing Polyploids

Perform a PCA on progeny

Description

Principal component analysis in order to identify individuals that deviate from the population.

Usage

PCA_progeny(dosage_matrix, highlight = NULL, colors = NULL, log = NULL)

Arguments

dosage_matrix	An integer matrix with markers in rows and individuals in columns.
highlight	A list of character vectors specifying individual names that should be highlighted
colors	Highlight colors. Vector of the same length as highlight.
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Details

Missing values are imputed by taking the mean of marker dosages per marker.

Examples

data("ALL_dosages")
PCA_progeny(dosage_matrix=ALL_dosages, highlight=list(c("P1", "P2")), colors="red")

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.