context("plot_peaks")
test_that("plot_peaks works", {
library(qtl2geno)
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))
map <- insert_pseudomarkers(iron$gmap, step=1)
probs <- calc_genoprob(iron, map, error_prob=0.002)
pheno <- iron$pheno
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)
Xcovar <- get_x_covar(iron)
library(qtl2scan)
out <- scan1(probs, pheno, addcovar=covar, Xcovar=Xcovar)
# find peaks above lod=3.5 (and calculate 1.5-LOD support intervals)
peaks <- find_peaks(out, map, threshold=3.5, drop=1.5)
test_plot_peaks <- function() plot_peaks(peaks, map)
vdiffr::expect_doppelganger("plot_peaks", test_plot_peaks)
})
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