Question: Homer log odds score calculation
1
4.5 years ago by
United States
Aishwarya Kulkarni40 wrote:

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        /0.2

 0.322 0.237 0.217 0.223 0.322 1.288 0.109916 0.419 0.25 0.207 0.123 0.419 1.676 0.224274 0.33 0.268 0.115 0.287 0.33 1.32 0.120574 0.014 0.955 0.014 0.017 0.955 3.82 0.582063 0.941 0.017 0.018 0.024 0.941 3.764 0.57565 0.02 0.02 0.913 0.047 0.913 3.652 0.562531 0.06 0.899 0.021 0.02 0.899 3.596 0.55582 0.022 0.019 0.017 0.942 0.942 3.768 0.576111 0.017 0.016 0.954 0.013 0.954 3.816 0.581608 0.244 0.1 0.288 0.368 0.368 1.472 0.167908 sum of max prob/0.25-> 4.05645

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

score homer • 1.5k views
written 4.5 years ago by Aishwarya Kulkarni40

Hey did you figure it out?