I am trying to import my list of motifs (that were output of MEME)

motifs<-importMatrix(file),
                     format="meme", 
                     to="pcm")

When I look at the result there is one more extra column than what I expect with an A value of 'NA'; the motif is only 8 bases long in this case.

Not sure why this is happening and how i can fix it 

Slot "mat":
  [,1] [,2]     [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A    0    1 0.000000    0    0    0    0    1   NA
C    1    0 0.290323    0    1    0    1    0    0
G    0    0 0.387097    1    0    1    0    0    1
T    0    0 0.322581    0    0    0    0    0    0

------------

my MEME file which is the input:

-----------------

MEME version 4.12.0

ALPHABET= ACGT

strands: + -

Background letter frequencies (from unknown source):
A 0.198 C 0.302 G 0.296 T 0.204

MOTIF CABGCGCA

letter-probability matrix: alength= 4 w= 8 nsites= 62 E= 8.6e-003
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.290323 0.387097 0.322581
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000

Well I solved this by doing the following:

for (i in 1:length(motifs)){
  motifs[[i]]@mat =motifs[[i]]@mat[,1:ncol(motifs[[i]]@mat)-1]
}

Hi Imolla,

Thank you for reporting this. This bug should be fixed in next building. 

Jianhong.