<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [

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  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
  <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
  <!ENTITY dhsurname   "<surname>Moeller</surname>">
  <!-- Please adjust the date whenever revising the manpage. -->
  <!ENTITY dhdate      "<date>April  6, 2004</date>">
  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
       allowed: see man(7), man(1). -->
  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
  <!ENTITY dhemail     "<email>moeller@pzr.uni-rostock.de</email>">
  <!ENTITY dhusername  "Steffen Moeller">
  <!ENTITY dhucpackage "<refentrytitle>CLUSTER3</refentrytitle>">
  <!ENTITY dhpackage   "cluster3">

  <!ENTITY debian      "<productname>Debian</productname>">
  <!ENTITY gnu         "<acronym>GNU</acronym>">
  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
]>

<refentry>
  <refentryinfo>
    <address>
      &dhemail;
    </address>
    <author>
      &dhfirstname;
      &dhsurname;
    </author>
    <copyright>
      <year>2003</year>
      <holder>&dhusername;</holder>
    </copyright>
    &dhdate;
  </refentryinfo>
  <refmeta>
    &dhucpackage;

    &dhsection;
  </refmeta>
  <refnamediv>
    <refname>&dhpackage;</refname>

    <refpurpose>Eisen-clustering of microarray data</refpurpose>
  </refnamediv>
  <refsynopsisdiv>
    <cmdsynopsis>
      <command>&dhpackage;</command>

      <arg><option>-f <replaceable>filename</replaceable></option></arg>
      <arg><option>-l <replaceable>0|1</replaceable></option></arg>
      <arg><option>-u <replaceable>jobname</replaceable></option></arg>
      <arg><option>-g <replaceable>[0..9]</replaceable></option></arg>
      <arg><option>-e <replaceable>[0..9]</replaceable></option></arg>
      <arg><option>-m <replaceable>[msca]</replaceable></option></arg>
      <arg><option>-k <replaceable>number</replaceable></option></arg>
      <arg><option>-s <replaceable>0|1</replaceable></option></arg>
      <arg><option>-x <replaceable>number</replaceable></option></arg>
      <arg><option>-y <replaceable>number</replaceable></option></arg>
    </cmdsynopsis>
  </refsynopsisdiv>
  <refsect1>
    <title>OPTIONS</title>

    <variablelist>
      <varlistentry><term><option>-h</option><option>--help</option></term><listitem><para>Show summary of options.</para></listitem></varlistentry>
      <varlistentry><term><option>-f <replaceable>filename</replaceable></option></term><listitem><para>file loding</para></listitem></varlistentry>
      <varlistentry><term><option>-u <replaceable>jobname</replaceable></option></term><listitem><para>Allows you to specify a different name for the output files (default is derived from the input file name)</para></listitem></varlistentry>
      <varlistentry><term><option>-l <replaceable>0|1</replaceable></option></term><listitem><para>Specifies whether to log-transform the data (default is 0, no log-transform)</para></listitem></varlistentry>
      <varlistentry><term><option>-k <replaceable>number</replaceable></option></term><listitem><para>Specifies whether to run k-means clustering instead of hierarchical clustering, and the number of clusters k to use (default: 0)</para></listitem></varlistentry>
      <varlistentry><term><option>-x <replaceable>number</replaceable></option></term><listitem><para>Specifies the horizontal dimension of the SOM grid (default: 2)</para></listitem></varlistentry>
      <varlistentry><term><option>-y <replaceable>number</replaceable></option></term><listitem><para>Specifies the vertical dimension of the SOM grid (default: 1)</para></listitem></varlistentry>
      <varlistentry><term><option>-s <replaceable>0|1</replaceable></option></term><listitem><para>Specifies whether to calculate an SOM instead of hierarchical clustering (default: 0)</para></listitem></varlistentry>
      <varlistentry>
        <term><option>-v</option>
          <option>--version</option>
        </term>
        <listitem>
          <para>Show version of program.</para>
        </listitem>
      </varlistentry>
    </variablelist>
<para>
  -g [0..9]     Specifies the distance measure for gene clustering
                0: No gene clustering
                1: Uncentered correlation
                2: Pearson correlation
                3: Uncentered correlation, absolute value
                4: Pearson correlation, absolute value
                5: Spearman's rank correlation
                6: Kendall's tau
                7: Euclidean distance
                8: Harmonically summed Euclidean distance
                9: City-block distance
                (default: 1)</para><para>
  -e [0..9]     Specifies the distance measure for microarray clustering
                0: No clustering
                1: Uncentered correlation
                2: Pearson correlation
                3: Uncentered correlation, absolute value
                4: Pearson correlation, absolute value
                5: Spearman's rank correlation
                6: Kendall's tau
                7: Euclidean distance
                8: Harmonically summed Euclidean distance
                9: City-block distance
                (default: 0)</para><para>
  -m [msca]     Specifies which hierarchical clustering method to use
                m: Pairwise complete-linkage
                s: Pairwise single-linkage
                c: Pairwise centroid-linkage
                a: Pairwise average-linkage
                (default: m)</para>
  </refsect1>
  <refsect1>
    <title>SEE ALSO</title>

    <para>mapletree (1), smile (1).</para>

  </refsect1>
  <refsect1>
    <title>AUTHOR</title>

    <para>This manual page was written by &dhusername; &dhemail; for
      the &debian; system (but may be used by others).  Permission is
      granted to copy, distribute and/or modify this document under
      the terms of the &gnu; General Public License, Version 2 any 
	  later version published by the Free Software Foundation.
    </para>
	<para>
	  On Debian systems, the complete text of the GNU General Public
	  License can be found in /usr/share/common-licenses/GPL.
	</para>

  </refsect1>
</refentry>

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