43 lines
No EOL
1.5 KiB
R
43 lines
No EOL
1.5 KiB
R
#' @title Compute Personal Freqs
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#' @description Laskee npops*(rowsFromInd*nloci) taulukon, jonka kutakin
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#' saraketta vastaa yksilön ind alleeli. Eri rivit ovat alleelin
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#' alkuperäfrekvenssit eri populaatioissa. Jos yksilölt?puuttuu jokin alleeli,
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#' niin vastaavaan kohtaa tulee sarake ykkösi?
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#' @param ind ind
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#' @param data data
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#' @param allFreqs allFreqs
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#' @param rowsFromInd rowsFromInd
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#' @export
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computePersonalAllFreqs <- function(ind, data, allFreqs, rowsFromInd) {
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if (is.null(dim(COUNTS))) {
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nloci <- npops <- 1
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} else {
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nloci <- ifelse(is.na(dim(COUNTS)[2]), 1, dim(COUNTS)[2])
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npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
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}
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rows <- as.matrix(t(data))[computeRows(rowsFromInd, ind, 1), , drop = FALSE]
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omaFreqs <- zeros(npops, rowsFromInd * nloci)
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pointer <- 1
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for (loc in 1:dim(rows)[2]) {
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for (all in 1:dim(rows)[1]) {
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if (rows[all, loc] >= 0) {
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if (pointer > ncol(omaFreqs)) omaFreqs <- cbind(omaFreqs, 0)
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omaFreqs[, pointer] <- tryCatch(
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matrix(
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data = as.matrix(t(allFreqs))[rows[all, loc], loc],
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nrow = npops
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),
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error = function(e) return(NA)
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)
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} else {
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omaFreqs[, pointer] <- ones(npops, 1)
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}
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# omaFreqs <- unname(cbind(omaFreqs, new_omaFreqs))
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pointer <- pointer + 1
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}
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}
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omaFreqs <- omaFreqs[, !is.na(omaFreqs)]
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return(omaFreqs)
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} |