t-test: p=0.748468
Neutral set average density: 0.00172608
Different set average density: 0.00177107
motif_present gene_set absent present different 631 363 neutral 1489 464
Fisher's exact test: p=6.97734e-13
Binomial GLM: p=4.4191e-13
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.9533 -0.7366 -0.7366 1.4194 1.6954
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.16598 0.05317 -21.930 < 2e-16 ***
differentTRUE 0.61307 0.08465 7.242 4.42e-13 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3498.3 on 2946 degrees of freedom
Residual deviance: 3446.4 on 2945 degrees of freedom
AIC: 3450.4
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.41731
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.3887 -0.7082 -0.5618 0.7261 2.0849
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.2516740 0.0830992 -27.096 <2e-16 ***
length 0.0051064 0.0002696 18.942 <2e-16 ***
differentTRUE 0.0782177 0.0964346 0.811 0.417
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3498.3 on 2946 degrees of freedom
Residual deviance: 2992.9 on 2944 degrees of freedom
AIC: 2998.9
Number of Fisher Scoring iterations: 4