t-test: p=5.75376e-59
Neutral set average density: 0.00630057
Different set average density: 0.00242816
motif_present gene_set absent present different 576 418 neutral 798 1155
Fisher's exact test: p=1.71391e-18
Binomial GLM: p=2.44883e-18
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.338 -1.338 1.025 1.025 1.316
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.36975 0.04603 8.032 9.56e-16 ***
differentTRUE -0.69037 0.07904 -8.734 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4072.0 on 2946 degrees of freedom
Residual deviance: 3994.6 on 2945 degrees of freedom
AIC: 3998.6
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=4.1049e-19
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.4980 -1.3105 0.9723 1.0437 1.3714
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.2857671 0.0607004 4.708 2.5e-06 ***
length 0.0004477 0.0002123 2.109 0.035 *
differentTRUE -0.7444967 0.0833320 -8.934 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4072.0 on 2946 degrees of freedom
Residual deviance: 3990.1 on 2944 degrees of freedom
AIC: 3996.1
Number of Fisher Scoring iterations: 4