Nothing
## compute pairwise fold changes
pairwise.logfc <- function (x, g, ave = mean, log = TRUE, base = 2, ...) {
g <- factor(g)
compare.levels <- function(i, j) {
xi <- x[as.integer(g) == i]
xj <- x[as.integer(g) == j]
if(log){
logFC <- ave(xj, ...) - ave(xi, ...)
}else{
logFC <- log(ave(xj, ...)/ave(xi, ...), base = base)
}
return(logFC)
}
ix <- seq_along(levels(g))
names(ix) <- levels(g)
pp <- outer(ix[-1], ix[-length(ix)], function(ivec, jvec) sapply(seq_along(ivec),
function(k) {
i <- ivec[k]
j <- jvec[k]
if (i > j)
compare.levels(i, j)
else NA
}))
pp <- pp[lower.tri(pp, diag = TRUE)]
nr <- length(levels(g))
Names <- numeric(choose(nr, 2))
Levels <- levels(g)
count <- 0
for(i in seq_len(nr-1))
for(j in (i+1):nr){
count <- count + 1
Names[count] <- paste(Levels[i], Levels[j], sep = " vs ")
}
names(pp) <- Names
return(pp)
}
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