The archive examples.zip contains some tracks and simple shell scripts. To run the examples:
1. Unpack the archive to a directory; copy the comiled program executable to the directory.
2. run the example shell files
3. find the results in the directory ./tracks/results (as defined in the cfg file)
4. after every run try to run R scripts (*.r)
5. look at the file 'statistics'. You can import this file to Excel (just copy-paste) or to R (read.table).

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Content:

human_chrom	-- human chromosome file

sg.cfg		-- example of configuration file that defines location of input tracks, binary profiles, and
		results. Some other parameters also defined.

two_track.sh	-- command line script comparing two tracks

five_track.sh	-- command line comparing five tracks that are given as file names in the command line. Every track will be compared to all other tracks in one direction (5*4/2=10 comparisons).

list_cmp.sh	-- command line for batch comparison of two lists of tracks. Here every track 
		from one list will be compared to each track from to enother list. There will be N*M comparisons.

h3k4me3_gene_start.sh -- command line for analysis of track H3K4me3 vs gene starts

pCorr.sh	-- Example of a partial correlation. The parameter 'pcorProfile=f_br.H3K4me1.wig'  
		can be placed into the config file.

LC.sh		-- Example of building the local correlation track 

heat_map_cc_for_statistics.r -- R script for drawing heatmap using statistics file

The folder LC-PolII-mRNA contains url's of two tracks: PolII and mRNA for IMR90 cell line, the script that can be run on dowloaded tracks and the result picture and table for LC.