t-test: p=2.13942e-09
Neutral set average density: 0.00627457
Different set average density: 0.00784665
motif_present gene_set absent present different 207 787 neutral 833 1120
Fisher's exact test: p=3.94725e-33
Binomial GLM: p=1.61582e-30
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.7714 -1.3054 0.6834 1.0546 1.0546
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.29605 0.04575 6.471 9.76e-11 ***
differentTRUE 1.03946 0.09053 11.482 < 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: 3826.5 on 2946 degrees of freedom
Residual deviance: 3682.2 on 2945 degrees of freedom
AIC: 3686.2
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0880009
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.4144 -0.8911 0.2436 0.8468 1.7044
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.5092038 0.0911370 -16.560 <2e-16 ***
length 0.0119766 0.0005895 20.317 <2e-16 ***
differentTRUE 0.1854616 0.1087089 1.706 0.088 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3826.5 on 2946 degrees of freedom
Residual deviance: 2851.6 on 2944 degrees of freedom
AIC: 2857.6
Number of Fisher Scoring iterations: 6