Nothing
context("align_scan1_map")
test_that("align_scan1_map works", {
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
# insert pseudomarkers into map
map <- insert_pseudomarkers(iron$gmap, step=1)
# calculate genotype probabilities
probs <- calc_genoprob(iron, map, error_prob=0.002)
# grab phenotypes and covariates; ensure that covariates have names attribute
pheno <- iron$pheno[,1]
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)
Xcovar <- get_x_covar(iron)
# genome scan
out <- scan1(probs, iron$pheno, Xcovar=Xcovar, addcovar=covar)
# calculate coefficients for chromosome 7
coef <- scan1coef(probs[,7], pheno, addcovar=covar)
# not subseted
result <- align_scan1_map(out, map)
expect_equal(result$scan1, out)
expect_equal(result$map, map)
# chr 7 for map
result <- align_scan1_map(out, map[7])
expect_equal( result$scan1, subset(out, map, chr="7") )
expect_equal( result$map, map[7] )
# chr 7 for scan
result <- align_scan1_map(subset(out,map,chr="7"), map)
expect_equal( result$scan1, subset(out, map, chr="7") )
expected_map <- map[7]
attr(expected_map, "is_x_chr") <- attr(map, "is_x_chr")[7]
expect_equal( result$map, expected_map )
# coefficients
result <- align_scan1_map(coef, map)
expect_equal( result$scan1, coef )
expected_map <- map[7]
attr(expected_map, "is_x_chr") <- attr(map, "is_x_chr")[7]
expect_equal( result$map, expected_map )
# shuffled output
out_attr <- attributes(out)
out_shuffled <- out[sample(1:nrow(out)),,drop=FALSE]
for(a in c("sample_size", "class"))
attr(out_shuffled, a) <- out_attr[[a]]
result <- align_scan1_map(out_shuffled, map)
expect_equal( result$scan1, out )
expect_equal( result$map, map )
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.