62 lines
No EOL
1.6 KiB
R
62 lines
No EOL
1.6 KiB
R
newGetDistances <- function(data, rowsFromInd) {
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ninds <- max(data[, ncol(data)])
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nloci <- size(data, 2) - 1
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riviLkm <- choose(ninds, 2)
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empties <- find(data < 0)
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data[empties] <- 0
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data <- apply(data, 2, as.numeric) # max(noalle) oltava <256
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pariTaulu <- zeros(riviLkm, 2)
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aPointer <- 1
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for (a in 1:(ninds - 1)) {
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pariTaulu_rows <- aPointer:(aPointer + ninds - 1 - a)
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pariTaulu[pariTaulu_rows, 1] <- ones(ninds - a, 1) * a
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pariTaulu[pariTaulu_rows, 2] <- t((a + 1):ninds)
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aPointer <- aPointer + ninds - a
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}
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eka <- pariTaulu[, ones(1, rowsFromInd)]
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eka <- eka * rowsFromInd
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miinus <- repmat((rowsFromInd - 1):0, c(riviLkm, 1))
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eka <- eka - miinus
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toka <- pariTaulu[, ones(1, rowsFromInd) * 2]
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toka <- toka * rowsFromInd
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toka <- toka - miinus
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summa <- zeros(riviLkm, 1)
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vertailuja <- zeros(riviLkm, 1)
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rm(pariTaulu, miinus)
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x <- zeros(size(eka))
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x <- apply(x, 2, as.integer)
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y <- zeros(size(toka))
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y <- apply(y, 2, as.integer)
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for (j in 1:nloci) {
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for (k in 1:rowsFromInd) {
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x[, k] <- data[eka[, k], j]
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y[, k] <- data[toka[, k], j]
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}
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for (a in 1:rowsFromInd) {
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for (b in 1:rowsFromInd) {
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vertailutNyt <- as.double(x[, a] > 0 & y[, b] > 0)
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vertailuja <- vertailuja + vertailutNyt
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lisays <- (x[, a] != y[, b] & vertailutNyt)
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summa <- summa + as.double(lisays)
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}
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}
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}
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rm(x, y, vertailutNyt)
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nollat <- find(vertailuja == 0)
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dist <- zeros(length(vertailuja), 1)
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dist[nollat] <- 1
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muut <- find(vertailuja > 0)
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dist[muut] <- summa[muut] / vertailuja[muut]
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rm(summa, vertailuja)
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Z <- linkage(t(dist))
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return(list(Z = Z, dist = dist))
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} |