t-test: p=2.32061e-38
Neutral set average density: 0.045852
Different set average density: 0.0374226
motif_present gene_set absent present different 1 993 neutral 12 1941
Fisher's exact test: p=0.072773
Binomial GLM: p=0.0814378
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.7153 0.0449 0.1110 0.1110 0.1110
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 5.0861 0.2896 17.564 <2e-16 ***
differentTRUE 1.8147 1.0415 1.742 0.0814 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 166.96 on 2946 degrees of freedom
Residual deviance: 161.94 on 2945 degrees of freedom
AIC: 165.94
Number of Fisher Scoring iterations: 9
Binomial GLM adjusted for length: p=0.607471
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.5970 0.0011 0.0196 0.0869 0.3723
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.85974 0.68458 2.717 0.006596 **
length 0.03872 0.01110 3.489 0.000486 ***
differentTRUE 0.53918 1.04963 0.514 0.607471
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 166.96 on 2946 degrees of freedom
Residual deviance: 131.82 on 2944 degrees of freedom
AIC: 137.82
Number of Fisher Scoring iterations: 12