modify_qtl {qtlpoly} | R Documentation |
Modify QTL model
Description
Adds or removes QTL manually from a given model.
Usage
modify_qtl(
model,
pheno.col = NULL,
add.qtl = NULL,
drop.qtl = NULL,
verbose = TRUE
)
## S3 method for class 'qtlpoly.modify'
print(x, pheno.col = NULL, ...)
Arguments
model |
an object of class |
pheno.col |
a phenotype column number whose model will be modified or printed. |
add.qtl |
a marker position number to be added. |
drop.qtl |
a marker position number to be removed. |
verbose |
if |
x |
an object of class |
... |
currently ignored |
Value
An object of class qtlpoly.modify
which contains a list of results
for each trait with the following components:
pheno.col |
a phenotype column number. |
stat |
a vector containing values from score statistics. |
pval |
a vector containing p-values from score statistics. |
qtls |
a data frame with information from the mapped QTL. |
Author(s)
Guilherme da Silva Pereira, gdasilv@ncsu.edu
References
Pereira GS, Gemenet DC, Mollinari M, Olukolu BA, Wood JC, Mosquera V, Gruneberg WJ, Khan A, Buell CR, Yencho GC, Zeng ZB (2020) Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population, Genetics 215 (3): 579-595. doi:10.1534/genetics.120.303080.
See Also
Examples
# Estimate conditional probabilities using mappoly package
library(mappoly)
library(qtlpoly)
genoprob4x = lapply(maps4x[c(5)], calc_genoprob)
data = read_data(ploidy = 4, geno.prob = genoprob4x, pheno = pheno4x, step = 1)
# Search for QTL
remim.mod = remim(data = data, pheno.col = 1, w.size = 15, sig.fwd = 0.0011493379,
sig.bwd = 0.0002284465, d.sint = 1.5, n.clusters = 1)
# Modify model
modified.mod = modify_qtl(model = remim.mod, pheno.col = 1, drop.qtl = 18)