Nothing
context("create snpinfo from cross2 object")
test_that("create_snpinfo works", {
skip_if(isnt_karl(), "this test only run locally")
file <- paste0("https://raw.githubusercontent.com/rqtl/",
"qtl2data/main/DOex/DOex.zip")
DOex <- read_cross2(file)
snpinfo <- create_snpinfo(DOex)
fg <- do.call("cbind", DOex$founder_geno)
expect_equal(sum(colSums(fg==0)==0), nrow(snpinfo))
n <- sapply(DOex$founder_geno, function(a) sum(colSums(a==0)==0))
expect_equivalent(unclass(table(snpinfo$chr)), n)
expect_equivalent(snpinfo$sdp, calc_sdp(t(fg[,colSums(fg==0)==0])))
})
test_that("create_snpinfo works for arab data", {
skip_if(isnt_karl(), "this test only run locally")
file <- paste0("https://raw.githubusercontent.com/rqtl/",
"qtl2data/main/ArabMAGIC/arabmagic_tair9.zip")
arab <- read_cross2(file)
snpinfo <- create_snpinfo(arab)
# expected markers, dropping non-informative or with missing founder genotype
tmp <- drop_nullmarkers(arab)
fg <- do.call("cbind", tmp$founder_geno)
fg <- fg[,colSums(is.na(fg) | fg==0) == 0]
expect_equal(nrow(snpinfo), ncol(fg))
expect_equal(rownames(snpinfo), colnames(fg))
})
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