t-test: p=4.0985e-27
Neutral set average density: 0.00165971
Different set average density: 0.000357468
motif_present gene_set absent present different 903 91 neutral 1615 338
Fisher's exact test: p=1.02356e-09
Binomial GLM: p=5.27577e-09
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.6165 -0.6165 -0.6165 -0.4382 2.1867
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.56404 0.05981 -26.148 < 2e-16 ***
differentTRUE -0.73082 0.12518 -5.838 5.28e-09 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2445.7 on 2946 degrees of freedom
Residual deviance: 2408.1 on 2945 degrees of freedom
AIC: 2412.1
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=9.94446e-11
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.8471 -0.6017 -0.5796 -0.4129 2.2801
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.7445805 0.0828322 -21.062 < 2e-16 ***
length 0.0009152 0.0002780 3.292 0.000994 ***
differentTRUE -0.8453499 0.1307014 -6.468 9.94e-11 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2445.7 on 2946 degrees of freedom
Residual deviance: 2397.8 on 2944 degrees of freedom
AIC: 2403.8
Number of Fisher Scoring iterations: 5