3069577ebd
Apparently that function is only used if the input is Genepop or BAPS format. However, its code might be useful for reducing some of the input of greedyMix(), as it contains the calculation for them.
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(c);
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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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