R version 4.5.0 beta (2025-04-02 r88102 ucrt) -- "How About a Twenty-Six"
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> library(oompaBase)
> # a key point is to test the matrixPairedT code
> # we create a simple example
> suppressWarnings( RNGversion("3.5.3") )
> set.seed(372284)
> nPairs <- 3
> nGenes <- 7
> m <- matrix(rnorm(2*nPairs*nGenes), ncol=2*nPairs)
> v <- factor(rep(c("A","B"), each=nPairs))
> pf <- rep(1:nPairs, 2)
> colnames(m) <- paste(as.character(v), pf, sep='')
> round(m, 2)
        A1    A2    A3    B1    B2    B3
[1,] -0.08 -1.18  0.75 -1.71  0.02  0.45
[2,] -0.86 -0.62  2.65  1.79 -0.40 -2.04
[3,] -1.74  2.21 -0.55 -0.21 -0.15  0.45
[4,]  0.03  0.24 -1.25  0.24 -0.28 -0.42
[5,] -1.63 -0.22  1.35  0.06  0.18 -1.35
[6,]  1.04 -1.94 -0.72 -0.36  1.03 -1.70
[7,]  0.36  0.73  0.70  3.91  0.29 -1.00
> # Now we run the package code
> mpt <- matrixPairedT(m, v, pf)
> # We also loop over the standard t.test function
> # for each gene
> realt <- sapply(1:nGenes, function(i) {
+   x <- m[i, v=="A"]
+   y <- m[i, v=="B"]
+   t1 <- t.test(y, x, paired=TRUE)
+   t1$statistic
+ })
> # The differences should all be less than 1e-15
> all(round(mpt-realt, 15) == 0)
[1] TRUE
> 
> # for completeness, we also check the unpaired result
> 
> mtt <- matrixT(m, v)
> realt <- sapply(1:nGenes, function(i) {
+   x <- m[i, v=="A"]
+   y <- m[i, v=="B"]
+   t1 <- t.test(x, y, paired=FALSE, var.equal=TRUE)
+   t1$statistic
+ })
> # The differences should all be less than 1e-15
> all(round(mtt-realt, 15) == 0)
[1] TRUE
> 
> # and the unequal variance case
> mut <- matrixUnequalT(m,v)
> realt <- sapply(1:nGenes, function(i) {
+   x <- m[i, v=="A"]
+   y <- m[i, v=="B"]
+   t1 <- t.test(x, y, paired=FALSE, var.equal=FALSE)
+   t1$statistic
+ })
> # The differences should all be less than 1e-15
> all(round(mut$tt-realt, 15) == 0)
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   0.25    0.07    0.34