Add thresholds to genome scan plot
Draw line segments at significance thresholds for a genome scan plot
add_threshold(map, thresholdA, thresholdX = NULL, chr = NULL, gap = NULL, ...)
map |
Marker map used in the genome scan plot |
thresholdA |
Autosomal threshold. Numeric or a list. (If a
list, the |
thresholdX |
X chromosome threshold (if missing, assumed to be the same as |
chr |
Chromosomes that were included in the plot |
gap |
Gap between chromosomes in the plot. Default is 1% of the total genome length. |
... |
Additional arguments passed to |
None.
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
map <- insert_pseudomarkers(iron$gmap, step=5)
probs <- calc_genoprob(iron, map, error_prob=0.002)
Xcovar <- get_x_covar(iron)
out <- scan1(probs, iron$pheno[,1], Xcovar=Xcovar)
# run just 3 permutations, as a fast illustration
operm <- scan1perm(probs, iron$pheno[,1], addcovar=Xcovar,
n_perm=3, perm_Xsp=TRUE, chr_lengths=chr_lengths(map))
plot(out, map)
add_threshold(map, summary(operm), col="violetred", lty=2)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.