Nothing
context("calc raw summaries")
test_that("calculation of raw summaries work", {
skip_if(isnt_karl(), "this test only run locally")
# load example data
file <- paste0("https://raw.githubusercontent.com/rqtl/",
"qtl2data/main/DOex/DOex.zip")
DOex <- read_cross2(file)
indIDs <- ind_ids(DOex)
mnames <- marker_names(DOex)
founder_ids <- rownames(DOex$founder_geno[[1]])
g <- do.call("cbind", DOex$geno)
fg <- do.call("cbind", DOex$founder_geno)
g[g==0] <- NA
fg[fg==0] <- NA
# calc_raw_het()
het <- calc_raw_het(DOex)
expect_equal(names(het), indIDs)
expect_true(all(het >= 0 & het <= 1))
expect_equal(het, rowMeans(g==2, na.rm=TRUE))
# calc_raw_maf() by marker
het <- calc_raw_het(DOex, "marker")
expect_equal(names(het), mnames)
expect_true(all(het >= 0 & het <= 1))
expect_equal(het, colMeans(g==2, na.rm=TRUE))
# calc_raw_maf()
maf_ind <- calc_raw_maf(DOex)
maf_mar <- calc_raw_maf(DOex, "marker")
expect_equal(names(maf_ind), indIDs)
expect_equal(names(maf_mar), mnames)
expect_equal(maf_ind, rowMeans(g==3, na.rm=TRUE) + rowMeans(g==2, na.rm=TRUE)/2)
expect_equal(maf_mar, colMeans(g==3, na.rm=TRUE) + colMeans(g==2, na.rm=TRUE)/2)
# calc_raw_founder_maf()
maf_ind <- calc_raw_founder_maf(DOex)
maf_mar <- calc_raw_founder_maf(DOex, "marker")
expect_equal(names(maf_ind), founder_ids)
expect_equal(names(maf_mar), mnames)
expect_equal(maf_ind, rowMeans(fg==3, na.rm=TRUE))
expect_equal(maf_mar, colMeans(fg==3, na.rm=TRUE))
# calc_raw_geno_freq()
gf_ind <- calc_raw_geno_freq(DOex)
gf_mar <- calc_raw_geno_freq(DOex, "marker")
expect_equal(dimnames(gf_ind), list(indIDs, c("AA", "AB", "BB")))
expect_equal(dimnames(gf_mar), list(mnames, c("AA", "AB", "BB")))
expect_equal(gf_ind, cbind(AA=rowMeans(g==1, na.rm=TRUE), AB=rowMeans(g==2, na.rm=TRUE), BB=rowMeans(g==3, na.rm=TRUE)))
expect_equal(gf_mar, cbind(AA=colMeans(g==1, na.rm=TRUE), AB=colMeans(g==2, na.rm=TRUE), BB=colMeans(g==3, na.rm=TRUE)))
# multi-core
gf_ind_2 <- calc_raw_geno_freq(DOex, cores=2)
gf_mar_2 <- calc_raw_geno_freq(DOex, "marker", cores=2)
expect_equal(gf_ind_2, gf_ind)
expect_equal(gf_mar_2, gf_mar)
})
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