t-test: p=0.363865
Neutral set average density: 0.00808311
Different set average density: 0.00779966
motif_present gene_set absent present different 229 765 neutral 741 1212
Fisher's exact test: p=1.71274e-16
Binomial GLM: p=7.57819e-16
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.7135 -1.3922 0.7237 0.9768 0.9768
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.49203 0.04663 10.551 < 2e-16 ***
differentTRUE 0.71413 0.08859 8.061 7.58e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3734.3 on 2946 degrees of freedom
Residual deviance: 3665.7 on 2945 degrees of freedom
AIC: 3669.7
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.428779
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.1614 -1.0179 0.3818 0.9261 1.5271
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.9468254 0.0826103 -11.461 <2e-16 ***
length 0.0094802 0.0005126 18.496 <2e-16 ***
differentTRUE -0.0827927 0.1046310 -0.791 0.429
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3734.3 on 2946 degrees of freedom
Residual deviance: 3040.2 on 2944 degrees of freedom
AIC: 3046.2
Number of Fisher Scoring iterations: 6