eHoPASA Files

eHoPASA extension for graphical presentation of homozygous regions over CMT
genes

Copyright 2010 by the Center for Medical Research, Medical University Graz.
Written by Slave Trajanoski.
For questions on EHoPASA, please contact Slave Trajanoski
(slave.trajanoski@medunigraz.at).

Charcot-Marie-Tooth (CMT) disease is a common group of inherited neuropathies
with autosomal dominant (ADCMT), autosomal recessive (ARCMT) or X-linked
inheritance. It has been shown that ARCMT, also known as CMT type 4 (CMT4), is
genetically heterogeneous with at least 14 genes identified so far.
This short R script helps you to visualize the homozygous regions discovered 
with eHoPASA over these regions. The script generates a single image file in 
PNG format.

Requirements
* installed and working version of the R statistical programming language
software version 2.10 or higher
* the script is tested only under Windows environment

All you have to do is run the following command in a working directory where 
the two additional text files coming with the script are also saved 
(chr_info_250K.txt and LGMD2_UCSC_250K.txt):

$path_to_R_executable\R.exe --slave --args arg1 arg2 arg3< graphic_CMT.r

argument1 - sample or field name from the report file with the number of 
consecutive homozygous genotypes
argument2 - title name for the diagram
argument3 - report file name

Notice: if you want to use empty space in your argument please enclose the 
argument with apostrophe ("argument").