To extract FUN-LDA scores the bigWigAverageOverBed utility is required.  It can be downloaded from the Genome Browser website at http://hgdownload.cse.ucsc.edu/admin/exe/.

Here is the current help page for this utility:
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bigWigAverageOverBed v2 - Compute average score of big wig over each bed, which may have introns.
usage:
   bigWigAverageOverBed in.bw in.bed out.tab
The output columns are:
   name - name field from bed, which should be unique
   size - size of bed (sum of exon sizes
   covered - # bases within exons covered by bigWig
   sum - sum of values over all bases covered
   mean0 - average over bases with non-covered bases counting as zeroes
   mean - average over just covered bases
Options:
   -stats=stats.ra - Output a collection of overall statistics to stat.ra file
   -bedOut=out.bed - Make output bed that is echo of input bed but with mean column appended
   -sampleAroundCenter=N - Take sample at region N bases wide centered around bed item, rather
                     than the usual sample in the bed item.
   -minMax - include two additional columns containing the min and max observed in the area.
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To use the utility, you must prepare a bed file, a tab-separated 4-column file.  The first column is the chromosome, the second is the zero-based coordinate of the position of interest, the third is that zero-based coordinate plus one, and the fourth is a unique identifier for the position.

Here is an example of the contents of a bed file, example.bed:

chr9    16885018        16885019        snp1

A bed file can have arbitrarily many rows.

Then bigWigAverageOverBed can be used as follows, assuming E059.valley9.c89.bigwig and example.bed are in the working directory:

bigWigAverageOverBed E059.valley9.c89.bigwig example.bed example.tab

It produces a 6-column file, example.tab, looking like this:

snp1    1       1       0.99999 0.99999 0.99999

The last column, average over the covered bases, is the score for this position.  The first column includes the unique id.  The -bedOut option to bigWigAverageOverBed can be used to include the other columns from the input .bed file in a .bed output file.