t-test: p=0.0629727
Neutral set average density: 0.0107813
Different set average density: 0.0114087
motif_present gene_set absent present different 110 884 neutral 533 1420
Fisher's exact test: p=9.50224e-26
Binomial GLM: p=1.70368e-22
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.0982 0.4843 0.4843 0.7984 0.7984
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.9799 0.0508 19.290 <2e-16 ***
differentTRUE 1.1041 0.1132 9.758 <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: 3092.0 on 2946 degrees of freedom
Residual deviance: 2981.1 on 2945 degrees of freedom
AIC: 2985.1
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0673567
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.3949 0.0212 0.3202 0.7435 1.3387
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.7264979 0.0989583 -7.341 2.11e-13 ***
length 0.0126788 0.0007646 16.582 < 2e-16 ***
differentTRUE 0.2353505 0.1286570 1.829 0.0674 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3092.0 on 2946 degrees of freedom
Residual deviance: 2421.4 on 2944 degrees of freedom
AIC: 2427.4
Number of Fisher Scoring iterations: 6