Creating a PWM from a PFM - redistribute gapped alignment count

Question

[Affan]

I have a position frequency matrix which I want to convert to a frequency weight matrix using the PWM() function of BioConductor in R.

The PFM is

A          271          342          445          1017          547           648          673          722          660          935          793          531
C          262          673          316          155           80            54           70           90           67           55           88           100
G          98           83           75           58            43            41           56           126          254          539          443          220
T          532          468          872          597           1046          891          991          855          879          267          412          153
M          0            0            0            0             0             0            0            0            0            0            0            0
R          0            0            0            0             0             0            0            0            0            0            0            0
W          0            0            0            0             0             0            0            0            0            0            0            0
S          0            0            0            0             0             0            0            0            0            0            0            0
Y          0            0            0            0             0             0            0            0            0            0            0            0
K          0            0            0            0             0             0            0            0            0            0            0            0
V          0            0            0            0             0             0            0            0            0            0            0            0
H          0            0            0            0             0             0            0            0            0            0            0            0
D          0            0            0            0             0             0            0            0            0            0            0            0
B          0            0            0            0             0             0            0            0            0            0            0            0
N          0            0            0            0             0             0            0            0            0            0            0            0
-          712          309          167          48            159           241          85           82           15           79           139          871
+          0            0            0            0             0             0            0            0            0            0            0            0
.          0            0            0            0             0             0            0            0            0            0            0            0

So now, the problem is that I have counts of "-" which came from the gapped alignment (done using ClustalW).

Now my main question is that would it be okay for me to redistribute the counts of "-" equally to the rest of the bases? I've also heard the suggestion of ignoring the "-" row and just using the PFM as the PWM. What would be a better solution for research? I believe I can redistribute the counts and be okay.