Nothing
context("expand snp association results to include all snps")
test_that("expand_snp_results() works", {
# this is a contrived example; basically a regression test
out_snps <- rbind(2.3417662372334, 4.6006054612920, 0.0260449600422, 0.7266312038275, 0.2121385389931)
dimnames(out_snps) <- list(c("rs221396738", "rs264175039", "rs229722012", "rs227574143", "rs27379133"),
"OF_immobile_pct")
class(out_snps) <- c("scan1", "matrix")
snpinfo <- data.frame(snp_id=c("rs221396738", "rs264175039", "rs227493750", "rs229722012",
"rs27379137", "rs227574143", "rs27379136", "rs216849408",
"rs240457950", "rs263973399", "rs27379135", "rs27379134",
"rs238531859", "rs27379133", "rs235268653", "rs260595137",
"rs219597400", "rs220959761", "rs241157930", "rs251406434"),
chr=rep("2", 20),
pos_Mbp=c(96.500012, 96.500224, 96.500276, 96.500343, 96.500437,
96.500668, 96.500749, 96.501004, 96.501091, 96.501096,
96.501138, 96.501283, 96.501312, 96.501406, 96.501861,
96.501951, 96.501980, 96.501993, 96.502069, 96.502099),
alleles=c("C|T", "A|C", "C|T", "C|G", "C|T",
"A|C", "A|C", "A|G", "C|A", "T|A",
"A|T", "A|C", "A|T", "A|T", "C|T",
"T|A", "C|T", "G|T", "A|C", "C|G"),
AJ=c(1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1),
B6=c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1),
"129"=c(1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1),
NOD=c(1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1),
NZO=c(1,3,3,3,1,3,3,3,3,3,3,3,1,3,1,1,1,1,1,1),
CAST=c(3,1,1,3,3,1,3,3,1,1,1,3,3,3,3,3,3,3,3,3),
PWK=c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1),
WSB=c(1,1,1,3,1,3,3,3,3,3,3,3,1,3,1,1,1,1,1,1),
sdp=c( 32, 16, 16, 176, 32, 144, 176, 176, 144, 144,
144, 176, 32, 189, 32, 32, 32, 32, 32, 32),
index=c(1, 2, 2, 4, 1, 6, 4, 4, 6, 6, 6, 4, 1,14, 1, 1, 1, 1, 1, 1),
stringsAsFactors=FALSE)
snp_map <- snpinfo_to_map(snpinfo)
index <- c(1,2,2,3,1,4,3,3,4,4,4,3,1,5,1,1,1,1,1,1)
expected <- list("lod"=cbind(unclass(out_snps)[,1][index]),
"map"=list("2"=snpinfo$pos))
rownames(expected$lod) <- names(expected$map[["2"]]) <- snpinfo$snp
colnames(expected$lod) <- "OF_immobile_pct"
expect_equal(expand_snp_results(out_snps, snp_map, snpinfo), expected)
})
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