You can use the wigToBigWig and bigWigCorrelate tools from UCSC (find the executable for your platform here).
First convert your WIG files to bigWig:
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.
Then correlate them:
bigWigCorrelate - Correlate bigWig files, optionally only on target regions.
bigWigCorrelate a.bigWig b.bigWig
-restrict=restrict.bigBed - restrict correlation to parts covered by this file
-threshold=N.N - clip values to this threshold