107 lines
4.1 KiB
R
107 lines
4.1 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 partitionCompare a list of partitions to compare
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#' @param npops number of populations
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#' @param counts counts
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#' @param sumcounts sumcounts
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#' @param max_iter maximum number of iterations
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#' @param alleleCodes allele codes
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#' @param inp input file
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#' @param popnames population names
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#' @param fixedK if \code{TRUE}, the number of populations is fixed
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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", "BAPS_clustering_diploid.txt", package = "rBAPS")
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#' greedyMix(data, "baps")
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greedyMix <- function(
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data, format = gsub("^.*\\.", "", data), partitionCompare = NULL, npops = 3L,
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counts = NULL, sumcounts = NULL, max_iter = 100L, alleleCodes = NULL,
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inp = NULL, popnames = NULL, fixedK = FALSE, verbose = FALSE
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) {
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# Importing and handling data ================================================
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# TODO: use format as class and make handling data a generic
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if (tolower(format) %in% "fasta") {
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data <- convert_FASTA_to_BAPS(data)
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format <- "baps"
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}
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if (tolower(format) %in% "baps") {
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data <- process_BAPS_data(data, NULL)
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c <- list(
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noalle = data[["noalle"]],
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data = data[["data"]],
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adjprior = data[["adjprior"]],
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priorTerm = data[["priorTerm"]],
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rowsFromInd = data[["rowsFromInd"]],
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Z = data[["Z"]],
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dist = data[["dist"]]
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)
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} else if (tolower(format) %in% "genepop") {
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data <- process_GenePop_data(data)
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c <- list(
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noalle = data[["noalle"]],
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data = data[["data"]],
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adjprior = data[["adjprior"]],
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priorTerm = data[["priorTerm"]],
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rowsFromInd = data[["rowsFromInd"]],
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Z = data[["Z"]],
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dist = data[["dist"]]
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)
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} else {
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data <- importFile(data, format, verbose)
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data <- handleData(data, tolower(format))
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c <- list(
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noalle = data[["noalle"]],
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data = data[["newData"]],
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adjprior = data[["adjprior"]],
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priorTerm = data[["priorTerm"]],
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rowsFromInd = data[["rowsFromInd"]],
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Z = data[["Z"]],
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dist = data[["dist"]]
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)
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}
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# Comparing partitions =======================================================
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ninds <- length(unique(c[["data"]][, ncol(c[["data"]])]))
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if (!is.null(partitionCompare)) {
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logmls <- comparePartitions(
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c[["data"]], nrow(c[["data"]]), partitionCompare[["partitions"]], ninds,
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c[["rowsFromInd"]], c[["noalle"]], c[["adjprior"]]
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)
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}
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# Generating partition summary ===============================================
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ekat <- seq(1L, ninds * c[["rowsFromInd"]], c[["rowsFromInd"]])
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c[["rows"]] <- cbind(ekat, ekat + c[["rowsFromInd"]] - 1L)
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logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose) # FIXME: not working for FASTA
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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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# Generating output object ===================================================
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out <- list(
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"alleleCodes" = alleleCodes, "adjprior" = c[["adjprior"]],
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"popnames" = popnames, "rowsFromInd" = c[["rowsFromInd"]],
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"data" = c[["data"]], "npops" = npops, "noalle" = c[["noalle"]],
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"mixtureType" = "mix", "logml" = logml
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)
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if (logml == 1) {
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return(out)
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}
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# Writing mixture info =======================================================
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changesInLogml <- writeMixtureInfo(
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logml, c[["rowsFromInd"]], c[["data"]], c[["adjprior"]], c[["priorTerm"]],
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NULL, inp, partitionSummary, popnames, fixedK, verbose
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)
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# Updateing results ==========================================================
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return(c(out, list("changesInLogml" = changesInLogml)))
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}
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