t-test: p=0.0801052
Neutral set average density: 0.00142717
Different set average density: 0.0011831
motif_present gene_set absent present different 766 228 neutral 1646 307
Fisher's exact test: p=2.4457e-06
Binomial GLM: p=1.74017e-06
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.7219 -0.7219 -0.5848 -0.5848 1.9237
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.67926 0.06217 -27.012 < 2e-16 ***
differentTRUE 0.46742 0.09776 4.781 1.74e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2792.1 on 2946 degrees of freedom
Residual deviance: 2769.6 on 2945 degrees of freedom
AIC: 2773.6
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.000609779
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.0220 -0.6664 -0.5722 -0.5479 1.9950
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.8732173 0.0809797 -23.132 < 2e-16 ***
length 0.0009778 0.0002487 3.931 8.46e-05 ***
differentTRUE 0.3510782 0.1024380 3.427 0.00061 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2792.1 on 2946 degrees of freedom
Residual deviance: 2754.8 on 2944 degrees of freedom
AIC: 2760.8
Number of Fisher Scoring iterations: 4