read.metagene: Metagene Data Input

In famuvie/breedR: Statistical Methods for Forest Genetic Resources Analysts

Description

A basic interface to the metagene simulator.

This function returns the data frame with the pedigree and phenotypes of the simulated individuals.

Usage

read.metagene(fname)

## S3 method for class 'metagene'
summary(object, ...)

## S3 method for class 'summary.metagene'
print(x, ...)

## S3 method for class 'metagene'
plot(x, type = c("default", "spatial"), ...)

## S3 method for class 'metagene'
get_ntraits(x, ...)

## S3 method for class 'metagene'
ngenerations(x, ...)

## S3 method for class 'metagene'
nindividuals(x, exclude.founders = FALSE, ...)

## S3 method for class 'metagene'
as.data.frame(x, ..., exclude.founders = TRUE)

Arguments

fname	file name of the second metagene output file (usually: insim.002)
object	a metagene object
...	not used
x	a metagene object
type	character. If 'default', the empirical density of the breeding and phenotypic values will be represented by generation. If 'spatial', the map of the spatial component will be plotted.
exclude.founders	logical: should the data.frame contain the genetic values of the founders?

Details

Read the output file (the one with the pedigree. Usually: insim.002) of the Metagene program, and build an object of class metagene.

Value

the data in the file as an object of class metagene

returns a data frame with one row per individual, with the spatial coordinates if applicable, the pedigree information, the generation, the true breeding value, the phenotype, the sex, the spatially structured component of the phenotype and other internal metagene variables.

Methods (by generic)

• summary: summary of a metagene object

• print: print summary method

• plot: plots either genetic and phenotypic values, or the spatial component of the phenotype. Pass further ggplot layers in ...

• get_ntraits: gets the number of traits

• ngenerations: gets the number of generations

• nindividuals: gets the number of individuals

• as.data.frame: Coerce to a data.frame

References

http://www.igv.fi.cnr.it/noveltree/

famuvie/breedR documentation built on Sept. 6, 2021, 4:50 a.m.