t-test: p=4.40555e-11
Neutral set average density: 0.0243958
Different set average density: 0.0205272
motif_present gene_set absent present different 52 942 neutral 218 1735
Fisher's exact test: p=5.1552e-08
Binomial GLM: p=2.53273e-07
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.4292 0.3278 0.4865 0.4865 0.4865
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 2.07427 0.07186 28.866 < 2e-16 ***
differentTRUE 0.82249 0.15954 5.155 2.53e-07 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1805.1 on 2946 degrees of freedom
Residual deviance: 1774.8 on 2945 degrees of freedom
AIC: 1778.8
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.0302068
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.6455 0.0228 0.1806 0.4862 1.1791
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.263000 0.150935 -1.742 0.0814 .
length 0.021856 0.001646 13.276 <2e-16 ***
differentTRUE -0.396624 0.182998 -2.167 0.0302 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1805.1 on 2946 degrees of freedom
Residual deviance: 1363.6 on 2944 degrees of freedom
AIC: 1369.6
Number of Fisher Scoring iterations: 8