Homer log odds score calculation
0
2
Entering edit mode
7.9 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 • 3.0k views
ADD COMMENT
1
Entering edit mode

Hey did you figure it out?

ADD REPLY

Login before adding your answer.

Traffic: 736 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6