t-test: p=3.18336e-06
Neutral set average density: 0.0611422
Different set average density: 0.0575511
motif_present gene_set absent present different 1 993 neutral 20 1933
Fisher's exact test: p=0.00402009
Binomial GLM: p=0.0230846
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.7153 0.0449 0.1435 0.1435 0.1435
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 4.5711 0.2248 20.338 <2e-16 ***
differentTRUE 2.3296 1.0254 2.272 0.0231 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 249.50 on 2946 degrees of freedom
Residual deviance: 238.85 on 2945 degrees of freedom
AIC: 242.85
Number of Fisher Scoring iterations: 9
Binomial GLM adjusted for length: p=0.278737
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.4161 0.0000 0.0016 0.0380 0.8280
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.75145 0.69599 -1.080 0.280
length 0.08229 0.01555 5.292 1.21e-07 ***
differentTRUE 1.13831 1.05091 1.083 0.279
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 249.50 on 2946 degrees of freedom
Residual deviance: 156.13 on 2944 degrees of freedom
AIC: 162.13
Number of Fisher Scoring iterations: 12