random_qtn_assign: random_qtn_assign

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

random_qtn_assign

Description

The function select random QTNs with certain criteria supplied as inputs.

Usage

random_qtn_assign(qtn,gen2phy,biased_selection,parental_genotypes,min_qtn_freq,dominant,effect_distribution,highest_P,lowest_P,high_to_low_percentage)

Arguments

qtn	Required: Number of QTNs to be selected
gen2phy	optinal: gen2phy object to calculate biased_selection
biased_selection	optional: if TRUE, the randomly selected QTNs are biased to gene density regions
parental_genotypes	Required: parental_genotypes object
min_qtn_freq	Optional: minimum QTN frequency, default is 0
dominant	Optional: a logical object for dominance, default is FALSE
h2	Optional: effect_distribution is "equal", "gamma", or "normal", default is "equal"
highest_P	Optional: the highest parent in case of using pick_parent method
lowest_P	Optional: the lowest parent in case of using pick_parent method
high_to_low_percentage	Optional: the percentage of opposite effect of lower parent, default 0

Value

randomly assigned QTNs and effects

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"
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)

USDA-ARS-GBRU/crossword documentation built on April 5, 2023, 7:29 p.m.