\name{import_RDP_cluster}
\alias{import_RDP_cluster}
\title{Import RDP cluster file and return otuTable (abundance table).}
\usage{
  import_RDP_cluster(RDP_cluster_file)
}
\arguments{
  \item{RDP_cluster_file}{A character string. The name of
  the \code{".clust"} file produced by the the complete
  linkage clustering step of the RDP pipeline.}
}
\value{
  An \code{\link{otuTable}} object parsed from the
  \code{".clust"} file.
}
\description{
  The RDP cluster pipeline (specifically, the output of the
  complete linkage clustering step) has no formal
  documentation for the \code{".clust"} file or its
  apparent sequence naming convention.
}
\details{
  \code{http://pyro.cme.msu.edu/index.jsp}

  The cluster file itself contains the names of all
  sequences contained in input alignment. If the upstream
  barcode and aligment processing steps are also done with
  the RDP pipeline, then the sequence names follow a
  predictable naming convention wherein each sequence is
  named by its sample and sequence ID, separated by a
  \code{"_"} as delimiter:

  \code{"sampleName_sequenceIDnumber"}

  This import function assumes that the sequence names in
  the cluster file follow this convention, and that the
  sample name does not contain any \code{"_"}. It is
  unlikely to work if this is not the case. It is likely to
  work if you used the upstream steps in the RDP pipeline
  to process your raw (barcoded, untrimmed) fasta/fastq
  data.

  This function first loops through the \code{".clust"}
  file and collects all of the sample names that appear. It
  secondly loops through each OTU (\code{"cluster"}; each
  row of the cluster file) and sums the number of sequences
  (reads) from each sample. The resulting abundance table
  of OTU-by-sample is trivially coerced to an
  \code{\link{otuTable}} object, and returned.
}
\references{
  \url{http://pyro.cme.msu.edu/index.jsp}
}