Hi,

I have used HOMER to identify a motif for a transcription factor I am studying. Now I would like to load this motif matrix into R and analyze it with bioconductor tools such as PWMEnrich. However, I can not figure out how to convert the HOMER format to .pfm. Has anyone seen a tool, or know how to do this?

A HOMER matrix looks like this:

>DATGASTCATHN	Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer	5.979652	-1205.524010	0	T:1427.0(49.57%),B:5654.9(12.14%),P:1e-523
0.305	0.134	0.316	0.245
0.486	0.214	0.275	0.025
0.001	0.001	0.001	0.997
0.001	0.001	0.946	0.052
0.997	0.001	0.001	0.001
0.047	0.454	0.452	0.048
0.001	0.001	0.001	0.997
0.052	0.946	0.001	0.001
0.997	0.001	0.001	0.001
0.025	0.278	0.213	0.484
0.243	0.327	0.131	0.300
0.256	0.266	0.231	0.247

And desired format of PFM file:

>MA0605.1    Atf3
A  [ 87 828   0   0 999   0 108  97 ]
C  [131   0   0   0   0 999   0 194 ]
G  [695 172   0 952   0   0 810  33 ]
T  [ 87   0 999  48   0   0  81 677 ]

Do you mean PCM (position count matrix)? To convert to pfm, you just transpose the matrix in R is OK. If you want PCM, you need total inputs number.