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Question: motifStack importMatrix problem reading meme file to pcm
1
gravatar for lmolla
5 months ago by
lmolla10
United States
lmolla10 wrote:

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

ADD COMMENTlink modified 5 months ago by Ou, Jianhong1.1k • written 5 months ago by lmolla10
0
gravatar for lmolla
5 months ago by
lmolla10
United States
lmolla10 wrote:

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]
}
ADD COMMENTlink written 5 months ago by lmolla10
0
gravatar for Ou, Jianhong
5 months ago by
Ou, Jianhong1.1k
United States
Ou, Jianhong1.1k wrote:

Hi Imolla,

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

Jianhong.

 

ADD COMMENTlink written 5 months ago by Ou, Jianhong1.1k
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