View source: R/random_qtn_assign.R
random_qtn_assign | R Documentation |
The function select random QTNs with certain criteria supplied as inputs.
random_qtn_assign(qtn,gen2phy,biased_selection,parental_genotypes,min_qtn_freq,dominant,effect_distribution,highest_P,lowest_P,high_to_low_percentage)
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 |
randomly assigned QTNs and effects
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)
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