% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/greedyMix.R
\name{greedyMix}
\alias{greedyMix}
\title{Clustering of individuals}
\usage{
greedyMix(
  data,
  format = gsub("^.*\\\\.", "", data),
  partitionCompare = NULL,
  npops = 1L,
  counts = NULL,
  sumcounts = NULL,
  max_iter = 100L,
  alleleCodes = NULL,
  inp = NULL,
  popnames = NULL,
  fixedK = FALSE,
  verbose = FALSE
)
}
\arguments{
\item{data}{data file}

\item{format}{Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop"}

\item{partitionCompare}{a list of partitions to compare}

\item{npops}{number of populations}

\item{counts}{counts}

\item{sumcounts}{sumcounts}

\item{max_iter}{maximum number of iterations}

\item{alleleCodes}{allele codes}

\item{inp}{input file}

\item{popnames}{population names}

\item{fixedK}{if \code{TRUE}, the number of populations is fixed}

\item{verbose}{if \code{TRUE}, prints extra output information}
}
\description{
Clustering of individuals
}
\examples{
\dontrun{ # TEMP: unwrap once #24 is resolved
data <- system.file("extdata", "BAPS_format_clustering_diploid.txt", package = "rBAPS")
greedyMix(data, "baps")
} # TEMP: unwrap once #24 is resolved
}
\references{
Samtools: a suite of programs for interacting
with high-throughput sequencing data. <http://www.htslib.org/>
}