getPhenotypes: Retrieve information about the phenotypes of the genetic...

In JanEngelstaedter/peas: Predicting patterns of Mendelian inheritance

Description

Retrieve information about the phenotypes of the genetic system

Usage

getPhenotypes(genopheno, equivalent = "phase", hideNoncanonical = TRUE)

Arguments

genopheno	a genopheno object containing all information about a genetic system.
equivalent	argument determining which genotypes are to be treated as equivalent. Possible options are "phase" (genotypes that differ only by phase are equivalent, i.e. the order of alleles within a locus does not matter), "origin" (phase is important but not the origin of alleles), and "none" (no two genotypes are equivalent).
hideNoncanonical	if this argument is set to TRUE (the default value), genotypes involving sex chromomal linkage groups that normally cannot arise (e.g., complete lack of an allele at an X-linked locus) are not displayed. If this argument is set to FALSE, even these noncanonical genotypes will be displayed.

Value

A dataframe in which rows represent genotypes (given by row names), and columns represent traits.

Examples

MendelsPeas <- newGenopheno(nloci = 1, alleleNames = list(c('Y', 'y')))
MendelsPeas <- setPhenotypes(MendelsPeas, 'colour', 'Y_', 'yellow')
MendelsPeas <- setPhenotypes(MendelsPeas, 'colour', 'yy', 'green')
getPhenotypes(MendelsPeas)

JanEngelstaedter/peas documentation built on May 5, 2019, 1:33 a.m.