phenotype: phenotype

In USDA-ARS-GBRU/crossword: Breeding program similation sotware

phenotype

Description

The function calculates phenotying for the input haplotype object using the QTN supplied effects.

Usage

phenotype(pop,qtn_effect,tgv_only,vr,parental_genotypes)

Arguments

pop	Required: a population
qtn_effect	Required: qtn_effect data frame
tgv_only	Required: if TRUE, only calculated breeding value will be export, without environmental effects, default is FALSE
vr	Required: Vr value
parental_genotypes	Required: parental_genotypes object

Value

Vr value

Examples

gff = "crossword_processing/peanut.gff"
chr_stat = "crossword_processing/chr_siz.txt"
chr_length = "crossword_processing/chr_len.txt"
gen2phy = physical2genomic(gff,chr_stat,chr_length,200000)
homo = TRUE
input_pheno = "crossword_processing/pheno.txt"
parental_genotypes = get_parental_genotypes(input,gen2phy,homo)
biased_selection = TRUE
min_qtn_freq = 0
dominant=FALSE
effect_distribution = "equal"
pop3 = create_families(pop=pop2,S=15,id="pop3",chr_length=chr_length)
qtn_effect = random_qtn_assign(qtn = 5,gen2phy=gen2phy,biased_selection=biased_selection,parental_genotypes=parental_genotypes,min_qtn_freq=min_qtn_freq,dominant=min_qtn_freq,effect_distribution=effect_distribution)
h2 = 0.6
tgv_only = FALSE

vr1 = get_vr(qtn_effect = qtn_effect,h2 = 0.6 ,parental_genotypes=parental_genotypes,dominant=TRUE,heritability_mode="absolute")
phen1 = get_vr(pop=pop3,qtn_effect=qtn_effect,vr=vr1)

USDA-ARS-GBRU/crossword documentation built on Oct. 11, 2024, 12:51 a.m.