######################################################################## @@@ @@@ @@@ @ @ @ @@@ @@@ @@@ @@@ @ @ @ @ @ @ @ @ @ @ @ @ @@@ @@@ @ @ @ @ @@@ @ @@@ @@ @ @ @ @ @ @ @ @ @ @ @ @ @ @@@ @@@ @@@ @@@ @ @@@ @ @ #TF-cluster#############################################################

##Table of Contents#####################################################

1............................................................Description

2..................................................................Usage

3...........................................................File Formats

4...............................................................Building

5.....................................................Build Requirements

6...........................................................Installation

7................................................................Credits

##Description########################################################### TF-cluster is a tool made to cluster data, originally designed to find interesting transcription factor co-expressions.

##Usage#################################################################

./triple-link-pthread -1 -2 -3 -t -e -k -c <"spearman" || "pearson">

Prints to stderr various status messages. Results are printed to stdout in the following format:

cluster 1:
<gene 1.1>
<gene 1.2>
...
<gene 1.M1>

cluster 2:
...

cluster N:
<gene N.1>
...
<gene N.MN>

##File Formats##########################################################

The settings file is no longer used, instead using command line arguments.

All input files expect UNIX standard line terminators.

The expression file used to generate the correlation matrix follows the format below:

<NAME 1> <EXPRESSION COEFFICIENT 1> <EC 2> ... <EC M>
<NAME 2> <EXPRESSION COEFFICIENT 1> <EC 2> ... <EC M>
...
<NAME N> <EXPRESSION COEFFICIENT 1> <EC 2> ... <EC M>

The transcription file, used to specify transcriptions factors from the expression file to create clusters from uses the following format:

<NAME 1>
<NAME 2>
...
<NAME N>

##Building##############################################################

make

##Build Requirements#################################################### gcc-libs madlib libc

##Installation##########################################################

make install

##Credits############################################################### Programmer: Josh Marshall [email protected]

Professor: Hairong Wei at [email protected]