In Bioconductor, Is it possible to create a PWM from DNA sequence alignment
with gaps to be used to scan sequences?

When I try it as suggested in "Biostrings" it gives the following error:

> pwm <- PWM(pfm)
Error in .normargPfm(x) :
  invalid PFM 'x': IUPAC ambiguity letters are represented

The help for "PWM" does say "with no IUPAC ambiguity letters" and Gaps are
ambiguity letters.

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Biostrings_2.28.0  IRanges_1.18.3     BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] stats4_3.0.1 tools_3.0.1

-best
-Lax

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