t-test: p=0.123208
Neutral set average density: 0.0135413
Different set average density: 0.0129731
motif_present gene_set absent present different 92 902 neutral 423 1530
Fisher's exact test: p=3.16959e-18
Binomial GLM: p=3.81936e-16
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.1817 0.4407 0.6987 0.6987 0.6987
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.28565 0.05493 23.404 < 2e-16 ***
differentTRUE 0.99718 0.12244 8.144 3.82e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2731.0 on 2946 degrees of freedom
Residual deviance: 2654.2 on 2945 degrees of freedom
AIC: 2658.2
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.920871
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.3096 0.0315 0.2926 0.6851 1.2960
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.5881560 0.1097609 -5.359 8.39e-08 ***
length 0.0149299 0.0009441 15.813 < 2e-16 ***
differentTRUE 0.0139503 0.1404351 0.099 0.921
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2731.0 on 2946 degrees of freedom
Residual deviance: 2119.6 on 2944 degrees of freedom
AIC: 2125.6
Number of Fisher Scoring iterations: 7