Homer log odds score calculation
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Entering edit mode
10.0 years ago

I was trying to figure out the log odds scoring system in homer for a motif, so if say for instance to calculate the log odds score for following pwm(given in homer library):

>NAHCAGCTGD Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer 6.116982 -5669.223213 0T:4676.0(58.38%),B:3979.3(10.04%),P:1e-2462
0.322 0.237 0.217 0.223
0.419 0.250 0.207 0.123
0.330 0.268 0.115 0.287
0.014 0.955 0.014 0.017
0.941 0.017 0.018 0.024
0.020 0.020 0.913 0.047
0.060 0.899 0.021 0.020
0.022 0.019 0.017 0.942
0.017 0.016 0.954 0.013
0.244 0.100 0.288 0.368


would it be ?

A         T         G         C         max      max prob  log of (max prob/0.25)
prob      /0.25
0.322     0.237     0.217     0.223     0.322    1.288     0.109915863
0.419     0.25      0.207     0.123     0.419    1.676     0.224274014
0.33      0.268     0.115     0.287     0.33     1.32      0.120573931
0.014     0.955     0.014     0.017     0.955    3.82      0.582063363
0.941     0.017     0.018     0.024     0.941    3.764     0.575649615
0.02      0.02      0.913     0.047     0.913    3.652     0.562530769
0.06      0.899     0.021     0.02      0.899    3.596     0.555819683
0.022     0.019     0.017     0.942     0.942    3.768     0.576110894
0.017     0.016     0.954     0.013     0.954    3.816     0.581608366
0.244     0.1       0.288     0.368     0.368    1.472     0.16790781
sum of max prob/0.25->     4.056454308


Is that how it is calculated? However the score in homer was 6.116982 ,so I wasn't sure if that's the case.

homer score • 3.6k views
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Entering edit mode

Hey did you figure it out?