Nothing
context("convert qtl2::scan1 to qtl::scanone output")
test_that("scan_qtl2_to_qtl works", {
library(qtl)
data(hyper)
hyper <- calc.genoprob(hyper[c(6,8),], step=2.5, err=0.01)
out_scanone <- scanone(hyper, method="hk")
# pull out pseudomarker map and adjust names
# (want to use the exact same map)
pmap <- lapply(hyper$geno, function(a) {
m <- attr(a$prob, "map")
m[grep("^loc", names(m))] })
for(i in seq(along=pmap))
names(pmap[[i]]) <- paste0("c", names(pmap)[i], ".",
names(pmap[[i]]))
library(qtl2)
hyper2 <- convert2cross2(hyper)
map <- insert_pseudomarkers(pull.map(hyper), pseudomarker_map=pmap)
pr <- calc_genoprob(hyper2, map, err=0.01)
out_scan1 <- scan1(pr, hyper$pheno[,1,drop=FALSE])
# adjustments to scanone output
colnames(out_scanone)[3] <- "bp"
for(atname in c("method", "type", "model"))
attr(out_scanone, atname) <- NULL
out_conv <- scan_qtl2_to_qtl(out_scan1, map)
expect_equal(out_conv, out_scanone)
})
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