t-test: p=1.09319e-07
Neutral set average density: 0.00603234
Different set average density: 0.00742688
motif_present gene_set absent present different 220 774 neutral 861 1092
Fisher's exact test: p=8.43982e-33
Binomial GLM: p=1.90249e-30
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.7367 -1.2799 0.7073 1.0783 1.0783
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.23767 0.04558 5.215 1.84e-07 ***
differentTRUE 1.02027 0.08896 11.468 < 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: 3873.8 on 2946 degrees of freedom
Residual deviance: 3730.9 on 2945 degrees of freedom
AIC: 3734.9
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0676724
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.9594 -0.8988 0.2526 0.8610 1.6984
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.500460 0.089011 -16.857 <2e-16 ***
length 0.011306 0.000556 20.333 <2e-16 ***
differentTRUE 0.194574 0.106489 1.827 0.0677 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3873.8 on 2946 degrees of freedom
Residual deviance: 2918.6 on 2944 degrees of freedom
AIC: 2924.6
Number of Fisher Scoring iterations: 6