Nothing
context("reduce to index snps")
test_that("reduce_to_index_snps works", {
# 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 <- 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(reduce_to_index_snps(snpinfo), snpinfo)
expect_equal(reduce_to_index_snps(snpinfo[snpinfo$chr==19,]), snpinfo[snpinfo$chr==19,])
expect_equal(reduce_to_index_snps(snpinfo[snpinfo$chr=="X",]), snpinfo[snpinfo$chr=="X",])
# 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$snp
snpinfo_extra <- rbind(snpinfo[,1:4], snpinfo_extra)
snpinfo_extra <- cbind(snpinfo_extra[c(1,8,7,2,3, 9,4,10,5,6),],
index=c(1,1,3,3,5, 1,1,3,4,3),
interval=c(91,91,91,91,132, 112,112,237,237,237),
on_map=c(FALSE,FALSE,FALSE,FALSE,TRUE, FALSE,FALSE,FALSE,FALSE,FALSE))
expected <- snpinfo_extra[c(1,3,5,6,8,9),]
expected$index <- c(1,2,3,1,2,3)
expect_equal(reduce_to_index_snps(snpinfo_extra), expected)
expect_equal(reduce_to_index_snps(snpinfo_extra[snpinfo_extra$chr==19,]), expected[expected$chr==19,])
expect_equal(reduce_to_index_snps(snpinfo_extra[snpinfo_extra$chr=="X",]), expected[expected$chr=="X",])
})
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