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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<title>The mcxalter manual</title>
</head>
<body>
<p style="text-align:right">
16 May 2014
<a class="local" href="mcxalter.ps"><b>mcxalter</b></a>
14-137
</p>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#name">NAME</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#synopsis">SYNOPSIS</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#description">DESCRIPTION</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#options">OPTIONS</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#author">AUTHOR</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#seealso">SEE ALSO</a>
</div>
</div>
<a name="name"></a>
<h2>NAME</h2>
<p style="margin-bottom:0" class="asd_par">
mcxalter — various network transformations</p>
<a name="synopsis"></a>
<h2>SYNOPSIS</h2>
<p style="margin-bottom:0" class="asd_par">
<b>mcxalter</b>
<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>specify matrix/graph input</i>)<b>]</b></a>
<a class="intern" href="#opt-abc"><b>[-abc</b> <fname> (<i>specify label input</i>)<b>]</b></a>
<a class="intern" href="#opt-tab"><b>[-tab</b> <fname> (<i>use tab file</i>)<b>]</b></a>
<a class="intern" href="#opt-icl"><b>[-icl</b> <fname> (<i>specify cluster input</i>)<b>]</b></a>
<a class="intern" href="#opt--block"><b>[--block</b> (<i>use within-cluster edges</i>)<b>]</b></a>
<a class="intern" href="#opt--blockc"><b>[--blockc</b> (<i>use between-cluster edges</i>)<b>]</b></a>
<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output</i>)<b>]</b></a>
<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
</p>
<a name="description"></a>
<h2>DESCRIPTION</h2>
<p style="margin-bottom:0" class="asd_par">
This utility supplies various transformations of networks.
</p>
<a name="options"></a>
<h2>OPTIONS</h2>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> <fname> (<i>label input</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
The file name for input that is in label format.</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<i>input matrix</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
The file name for input that is in mcl native matrix format.</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> <fname> (<i>use tab file</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
This option causes the output to be printed with the labels
found in the tab file.
With <b>-abc</b> this option will, additionally, construct
a graph only on the labels found in the tab file.
If this option is used in conjunction with <b>-imx</b> the
tab domain and the matrix domain are required to be identical.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> <fname> (<i>specify cluster input</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Read in a cluster file for use with either <b>--block</b> or <b>--blockc</b>.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--block"></a><b>--block</b> (<i>use within-cluster edges</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Remove between-cluster edges from the network. This is done first, before
other transformations take effect.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--blockc"></a><b>--blockc</b> (<i>use between-cluster edges</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Remove within-cluster edges from the network. This is done first, before
other transformations take effect.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> <tf-spec> (<i>transform input matrix values</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Transform the input matrix values according
to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Output file.</p>
</div>
</div>
<a name="author"></a>
<h2>AUTHOR</h2>
<p style="margin-bottom:0" class="asd_par">
Stijn van Dongen.
</p>
<a name="seealso"></a>
<h2>SEE ALSO</h2>
<p style="margin-bottom:0" class="asd_par">
<a class="local sibling" href="mcxio.html">mcxio</a>,
<a class="local sibling" href="mcx.html">mcx</a>,
<a class="local sibling" href="mcxsubs.html">mcxsubs</a>,
and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
and the utilities in the mcl family.
</p>
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