plot_sint {qtlpoly} | R Documentation |
QTLs with respective support interval plots
Description
Creates a plot where colored bars represent the support intervals for QTL peaks (black dots).
Usage
plot_sint(data, model, pheno.col = NULL, main = NULL, drop = FALSE)
Arguments
data |
an object of class |
model |
an object of class |
pheno.col |
a numeric vector with the phenotype column numbers to be plotted; if |
main |
a character string with the main title; if |
drop |
if |
Value
A ggplot2 with QTL bars for each linkage group.
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)
# Plot support intervals
plot_sint(data = data, model = remim.mod)