data(for.exercise, package="snpStats")
n <- 700
m <- 20000
context("dups")
x <- snps.10[c(1:n,1:n),1:m]
y <- snps.10[c(1:1000),1:m]
rownames(x) <- paste("x",make.unique(rownames(x)),sep="")
rownames(y) <- paste("y",make.unique(rownames(y)),sep="")
test_that("dups works", {
system.time(kk.slow <- dups(x,y,tol=10,stopatone=FALSE))
system.time(kk.quick <- dups(x,y,tol=10,stopatone=TRUE))
expect_true(nrow(kk.slow) == 2*n) # finds both matches
expect_true(nrow(kk.quick) == n) # finds first match
})
## system.time(kk<-dups(x,y))
## system.time(ll<-dups.c(x,y))
## hist(kk,breaks=m)
## hist(diag(kk),breaks=m,xlim=c(0,m))
## hist(kk[upper.tri(kk)],breaks=m,xlim=c(0,m))
## hist(kk[lower.tri(kk)],breaks=m,xlim=c(0,m))
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