t-test: p=0.190313
Neutral set average density: 0.000168298
Different set average density: 0.000218332
motif_present gene_set absent present different 922 72 neutral 1880 73
Fisher's exact test: p=6.36214e-05
Binomial GLM: p=4.34203e-05
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.3878 -0.3878 -0.2760 -0.2760 2.5638
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.2486 0.1193 -27.232 < 2e-16 ***
differentTRUE 0.6987 0.1709 4.088 4.34e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1156.2 on 2946 degrees of freedom
Residual deviance: 1139.8 on 2945 degrees of freedom
AIC: 1143.8
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.220861
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.3888 -0.3115 -0.2351 -0.2013 2.8348
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -4.2260469 0.1699079 -24.873 <2e-16 ***
length 0.0038329 0.0003535 10.844 <2e-16 ***
differentTRUE 0.2220868 0.1814075 1.224 0.221
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1156.2 on 2946 degrees of freedom
Residual deviance: 1033.2 on 2944 degrees of freedom
AIC: 1039.2
Number of Fisher Scoring iterations: 6