trait.architecture: Define the trait architecture

In UMN-BarleyOatSilphium/GSSimTPUpdate: Code and data to accompany the publication [TITLE]

Description

Adds QTL to a genome. SNPs are assigned (randomly or by the user) to become QTL. Effects are then assigned to the QTL (from various distributions). All QTL have additive effects, and some, all, or none can have dominance effects.

Usage

trait.architecture(genome, n.QTL, qtl.index = NULL, qtl.dom.index = NULL,
  qtl.perf.index = NULL, qtl.add.eff = "normal", qtl.dom.eff = NULL)

Arguments

genome	The list of hypred genomes.
n.QTL	The number of SNPs to become QTL.
qtl.index	A list of SNP indices per chromosome to become QTL. If NULL, indices are randomly sampled.
qtl.dom.index	A list of QTL indices per chromosome to have dominance effects.
qtl.perf.index	A list of QTL indices per chromosome to be perfect markers (i.e. the observed SNP is the QTL).
qtl.add.eff	A vector of length n.QTL of additive effects of QTL. The vector is interpreted as such: the ith element in the vector will be the additive effect assigned to the ith QTL. Can also be "normal" to draw effects from a standard normal distribution or "geometric" to draw effects from a geometric series.
qtl.dom.eff	A vector of length n.QTL of dominance effects of QTL. The vector is interpreted as such: the ith element in the vector will be the dominance effect assigned to the ith QTL.

Value

A list of hypred genomes with assigned trait architecture.

UMN-BarleyOatSilphium/GSSimTPUpdate documentation built on May 9, 2019, 7:40 p.m.