16 lines
611 B
R
16 lines
611 B
R
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#' @title Convert from FASTA to BAPS
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#' @description Converts a file (not an R object) from FASTA to BAPS format
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#' @param file filename of FASTA file
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#' @return `data` in BAPS format
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#' @author Waldir Leoncio
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#' @export
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#' @examples
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#' file <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
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#' convert_FASTA_to_BAPS(file)
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convert_FASTA_to_BAPS <- function(file) {
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data <- load_fasta(file) # Processing data
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data <- cbind(data, seq_len(nrow(data))) # Add IDs of individuals (sequential)
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data[data == 0] <- -9 # Because zeros (missing) in BAPS are coded as -9
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return(data)
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}
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