t-test: p=1.40111e-18
Neutral set average density: 0.00266774
Different set average density: 0.00122065
motif_present gene_set absent present different 738 256 neutral 1392 561
Fisher's exact test: p=0.0898211
Binomial GLM: p=0.0886728
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.8229 -0.8229 -0.7717 1.5795 1.6471
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.90878 0.05001 -18.172 <2e-16 ***
differentTRUE -0.14999 0.08810 -1.702 0.0887 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3479.3 on 2946 degrees of freedom
Residual deviance: 3476.4 on 2945 degrees of freedom
AIC: 3480.4
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=5.94718e-07
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.6708 -0.7819 -0.7080 1.2022 1.9920
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.4225000 0.0694547 -20.481 < 2e-16 ***
length 0.0025645 0.0002267 11.313 < 2e-16 ***
differentTRUE -0.4778011 0.0956956 -4.993 5.95e-07 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3479.3 on 2946 degrees of freedom
Residual deviance: 3344.5 on 2944 degrees of freedom
AIC: 3350.5
Number of Fisher Scoring iterations: 4