Produce a table that correlates all pairs of wig or bigWig files
wigCorrelate [options] one.wig two.wig ... n.wig
This tool is part of UCSC Genome Browser's utilities.
wigCorrelate works by finding items that overlap in the different wig or bigwig files. Within the overlap it considers each base a separate observation and calculates Pearson's R based on that. The output is to stdout.
wigCorrelate to calculate pairwise Pearson's $R$ among three bigwig files (a.bw, b.bw, and c.bw):
wigCorrelate a.bigWig b.bigWig c.bigWig
Results like the following will be printed to your screen (the default stdout)
a.bigWig b.bigWig 0.406864 a.bigWig c.bigWig 0.455641 b.bigWig c.bigWig 0.591586