Nothing
optimclass <- function (comm, stride, pval = 0.01, counts = 2)
{
if (!inherits(stride,'stride'))
stop("The second argument must be of class 'stride'")
strides <- ncol(stride$clustering)
mondo.fisher <- function(comm, clust) {
rows <- ncol(comm)
cols <- length(table(clust))
res <- matrix(NA, nrow = rows, ncol = cols)
for (i in 1:rows) {
for (j in 1:cols) {
res[i, j] <- fisher.test(comm[, i] > 0, clust ==
j)$p.val
}
}
res
}
vals <- rep(NA, strides)
cts <- rep(NA, strides)
for (i in 1:strides) {
tmp <- mondo.fisher(comm = comm, clust = stride$clustering[,
i])
vals[i] <- sum(tmp <= pval)
cts[i] <- sum(apply(tmp <= pval, 2, sum) >= counts)
}
out <- data.frame(stride$seq,vals,cts)
names(out) <- c('clusters','sig.spc','sig.clust')
attr(out, "call") <- match.call()
attr(out, "timestamp") <- date()
out
}
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