52 lines
2 KiB
R
52 lines
2 KiB
R
#' @title Clustering of individuals
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#' @param data data file
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#' @param format Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop"
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#' @param verbose if \code{TRUE}, prints extra output information
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#' @importFrom utils read.delim
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#' @importFrom vcfR read.vcfR
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#' @importFrom Rsamtools scanBam
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#' @importFrom adegenet read.genepop .readExt
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#' @references Samtools: a suite of programs for interacting
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#' with high-throughput sequencing data. <http://www.htslib.org/>
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#' @export
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#' @examples
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#' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
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#' greedyMix(data)
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greedyMix <- function(
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data, format, c.rows, partitionCompare.partitions, ninds, rowsFromInd, noalle,
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adjprior, priorTerm, alleleCodesinp, popnames, fixedK = FALSE,
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partition_compare = FALSE, verbose = TRUE
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) {
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# Importing and handling data ================================================
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data <- importFile(data, format, verbose)
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if (partition_compare) {
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logmls <- comparePartitions(
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data, c.rows, partitionCompare.partitions, ninds, rowsFromInd, noalle,
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adjprior
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)
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}
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# Generating partition summary ===============================================
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logml_npops_partitionSummary <- indMixWrapper(data, npops, fixedK);
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logml <- logml_npops_partitionSummary[["logml"]]
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npops <- logml_npops_partitionSummary[["npops"]]
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partitionSummary <- logml_npops_partitionSummary[["partitionSummary"]]
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stopifnot(logml != 1)
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# Writing mixture info =======================================================
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changesInLogml <- writeMixtureInfo(
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logml, rowsFromInd, data, adjprior, priorTerm, NULL, inp, partitionSummary,
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popnames, fixedK
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)
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# Returning results ==========================================================
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return(
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list(
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"alleleCodes" = alleleCodes, "adjprior" = adjprior, "popnames" = popnames,
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"rowsFromInd" = rowsFromInd, "data" = data, "npops" = npops,
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"noalle" = noalle, "mixtureType" = "mix", "logml" = logml,
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"changesInLogml" = changesInLogml
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)
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)
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}
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