context("applyToCisPairs")
test_that("applyToCisPairs runs on small example", {
rangesGR <- GenomicRanges::GRanges(
rep(c("chr1", "chr2"), c(3,2)),
IRanges::IRanges(
c(100, 200, 300, 100, 200),
c(150, 250, 350, 150, 250)
))
gp <- data.frame(
g1=c(1,4,2,1,4),
g2=c(2,4,3,3,5)
)
datamat <- rbind(
c(10, 20, 30),
c(15, 26, 40),
c(100, 2, 0),
c(10, 20, 30),
c(15, 26, 40)
)
corVal <- applyToCisPairs(gp, rangesGR, datamat)
expect_equal(length(corVal), 5)
expect_equal(corVal[2], 1)
expect_equal(corVal[1], cor(datamat[1,], datamat[2,]))
expect_equal(corVal, sapply(1:nrow(gp),
function(i){
cor(datamat[gp[i, 1], ], datamat[gp[i, 2], ])
}))
})
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