Nothing
context("index snps")
test_that("index_snps works", {
skip_if(isnt_karl(), "this test only run locally")
# load example data and calculate genotype probabilities
file <- paste0("https://raw.githubusercontent.com/rqtl/",
"qtl2data/main/DO_Recla/recla.zip")
recla <- read_cross2(file)
# founder genotypes for a set of SNPs
snpgeno <- rbind(m1=c(3,1,1,3,1,1,1,1),
m2=c(1,3,1,3,1,3,1,3),
m3=c(1,1,1,1,3,3,3,3),
m4=c(1,3,1,3,1,3,1,3),
m5=c(1,1,1,3,1,3,1,1),
m6=c(1,1,3,1,1,1,3,1))
sdp <- calc_sdp(snpgeno)
snpinfo <- data.frame(chr=c("19", "19", "X", "X", "19", "X"),
pos=c(40.36, 40.53, 110.91, 111.21, 56.480843, 56.480843),
sdp=sdp,
snp=c("m1", "m2", "m3", "m4", "m5", "m6"), stringsAsFactors=FALSE)
snpinfo_windex <- index_snps(recla$pmap, snpinfo)
snpinfo19_windex <- index_snps(recla$pmap, snpinfo[snpinfo$chr=="19",])
snpinfoX_windex <- index_snps(recla$pmap, snpinfo[snpinfo$chr=="X",])
expected <- cbind(snpinfo[c(1,2,5,6,3,4),],
index=c(1:3, 1:3),
interval=c(91,91,132,112,237,237),
on_map=c(FALSE, FALSE, TRUE, FALSE, FALSE, FALSE))
expect_equal(snpinfo_windex, rbind(snpinfo19_windex, snpinfoX_windex))
expect_equal(snpinfo_windex, expected)
expect_equal(snpinfo19_windex, expected[1:3,])
expect_equal(snpinfoX_windex, expected[4:6,])
# repeat with some redundant snps
snpinfo_extra <- data.frame(chr=c("19", "19", "X", "X"),
pos=c(40.45, 40.37, 56.3, 110.83),
sdp=c(170, 9, 68, 170),
snp=c("m7", "m8", "m9", "m10"),
stringsAsFactors=FALSE)
rownames(snpinfo_extra) <- snpinfo_extra$snp
snpinfo <- rbind(snpinfo, snpinfo_extra)
expected <- cbind(snpinfo[c(1,8,7,2,5, 9,6,10,3,4),],
index=c(1,1,3,3,5, 1,1,3,4,3),
interval=c(91,91,91,91,132, 112,112,237,237,237),
on_map=c(FALSE,FALSE,FALSE,FALSE,TRUE, FALSE,FALSE,FALSE,FALSE,FALSE))
snpinfo_windex <- index_snps(recla$pmap, snpinfo)
snpinfo19_windex <- index_snps(recla$pmap, snpinfo[snpinfo$chr=="19",])
snpinfoX_windex <- index_snps(recla$pmap, snpinfo[snpinfo$chr=="X",])
expect_equal(snpinfo_windex, rbind(snpinfo19_windex, snpinfoX_windex))
expect_equal(snpinfo_windex, expected)
expect_equal(snpinfo19_windex, expected[1:5,])
expect_equal(snpinfoX_windex, expected[6:10,])
})
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.