t-test: p=0.0594278
Neutral set average density: 0.000536746
Different set average density: 0.000400871
motif_present gene_set absent present different 870 124 neutral 1795 158
Fisher's exact test: p=0.000197739
Binomial GLM: p=0.000145687
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.5162 -0.5162 -0.4108 -0.4108 2.2426
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.43017 0.08298 -29.285 < 2e-16 ***
differentTRUE 0.48195 0.12689 3.798 0.000146 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1859.6 on 2946 degrees of freedom
Residual deviance: 1845.5 on 2945 degrees of freedom
AIC: 1849.5
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.574394
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.5014 -0.4394 -0.3590 -0.3189 2.5183
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.2004953 0.1166880 -27.428 <2e-16 ***
length 0.0032963 0.0002841 11.601 <2e-16 ***
differentTRUE 0.0761458 0.1355894 0.562 0.574
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1859.6 on 2946 degrees of freedom
Residual deviance: 1719.3 on 2944 degrees of freedom
AIC: 1725.3
Number of Fisher Scoring iterations: 5