2020-05-20 11:22:31 +02:00
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/greedyMix.R
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\name{greedyMix}
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\alias{greedyMix}
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\title{Clustering of individuals}
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\usage{
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greedyMix(
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data,
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format = gsub("^.*\\\\.", "", data),
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partitionCompare = NULL,
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npops = 1L,
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counts = NULL,
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sumcounts = NULL,
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max_iter = 100L,
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alleleCodes = NULL,
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inp = NULL,
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popnames = NULL,
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fixedK = FALSE,
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verbose = FALSE
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)
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}
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\arguments{
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\item{data}{data file}
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\item{format}{Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop"}
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\item{partitionCompare}{a list of partitions to compare}
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\item{npops}{number of populations}
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\item{counts}{counts}
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\item{sumcounts}{sumcounts}
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\item{max_iter}{maximum number of iterations}
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\item{alleleCodes}{allele codes}
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\item{inp}{input file}
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\item{popnames}{population names}
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\item{fixedK}{if \code{TRUE}, the number of populations is fixed}
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\item{verbose}{if \code{TRUE}, prints extra output information}
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}
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\description{
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Clustering of individuals
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}
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\examples{
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\dontrun{ # TEMP: unwrap once #24 is resolved
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data <- system.file("extdata", "BAPS_format_clustering_diploid.txt", package = "rBAPS")
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greedyMix(data, "baps")
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} # TEMP: unwrap once #24 is resolved
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}
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\references{
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Samtools: a suite of programs for interacting
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with high-throughput sequencing data. <http://www.htslib.org/>
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}
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