t-test: p=5.24513e-12
Neutral set average density: 0.00285514
Different set average density: 0.00411238
motif_present gene_set absent present different 369 625 neutral 1227 726
Fisher's exact test: p=3.6141e-40
Binomial GLM: p=6.99408e-39
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.4078 -0.9641 -0.9641 0.9633 1.4068
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.52478 0.04682 -11.21 <2e-16 ***
differentTRUE 1.05173 0.08064 13.04 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4065.0 on 2946 degrees of freedom
Residual deviance: 3888.8 on 2945 degrees of freedom
AIC: 3892.8
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.00164567
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.2340 -0.7335 -0.5283 0.7834 2.0913
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.3460462 0.0918891 -25.531 < 2e-16 ***
length 0.0099413 0.0004334 22.938 < 2e-16 ***
differentTRUE 0.3129278 0.0994151 3.148 0.00165 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4065.0 on 2946 degrees of freedom
Residual deviance: 2920.8 on 2944 degrees of freedom
AIC: 2926.8
Number of Fisher Scoring iterations: 5