52 lines
1.5 KiB
R
52 lines
1.5 KiB
R
#' @title Add Alleles
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#' @param data data
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#' @param ind ind
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#' @param line line
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#' @param divider divider
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#' @return data (after alleles were added)
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#' @export
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addAlleles <- function(data, ind, line, divider) {
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# Lisaa BAPS-formaatissa olevaan datataulukkoon
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# yksil<69><6C> ind vastaavat rivit. Yksil<69>n alleelit
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# luetaan genepop-formaatissa olevasta rivist?
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# line. Jos data on 3 digit formaatissa on divider=1000.
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# Jos data on 2 digit formaatissa on divider=100.
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nloci <- size(data, 2) # added 1 from original code
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if (size(data, 1) < (2 * ind)) {
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data <- rbind(data, zeros(100, nloci)) # subtracted 1 from original code
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}
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k <- 1
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merkki <- substring(line, k, k)
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while (merkki != ",") {
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k <- k + 1
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merkki <- substring(line, k, k)
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}
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line <- substring(line, k + 1)
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# clear k; clear merkki;
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if (grepl(" ", line)) {
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alleeliTaulu <- as.numeric(strsplit(line, split = " ")[[1]])
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} else if (grepl("\t", line)) {
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alleeliTaulu <- as.numeric(strsplit(line, split = "\t")[[1]])
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}
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if (length(alleeliTaulu) != nloci) {
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stop("Incorrect data format.")
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}
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for (j in seq_len(nloci)) {
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ekaAlleeli <- floor(alleeliTaulu[j] / divider)
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if (is.na(ekaAlleeli) | ekaAlleeli == 0) ekaAlleeli <- -999
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tokaAlleeli <- alleeliTaulu[j] %% divider
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if (is.na(tokaAlleeli) | tokaAlleeli == 0) tokaAlleeli <- -999
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data[2 * ind - 1, j] <- ekaAlleeli
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data[2 * ind, j] <- tokaAlleeli
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}
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data[2 * ind - 1, ncol(data)] <- ind
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data[2 * ind, ncol(data)] <- ind
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return(data)
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}
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