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Question: motifStack importMatrix problem reading meme file to pcm
1
7 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

modified 7 months ago by Ou, Jianhong1.1k • written 7 months ago by lmolla10
0
7 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]
}
0
7 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.