t-test: p=7.21769e-05
Neutral set average density: 0.00897969
Different set average density: 0.0101887
motif_present gene_set absent present different 125 869 neutral 632 1321
Fisher's exact test: p=1.16453e-33
Binomial GLM: p=3.5808e-29
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.0364 -1.5022 0.5184 0.8843 0.8843
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.73725 0.04837 15.24 <2e-16 ***
differentTRUE 1.20177 0.10719 11.21 <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: 3358.2 on 2946 degrees of freedom
Residual deviance: 3211.0 on 2945 degrees of freedom
AIC: 3215
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0542049
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.7657 -0.8365 0.2271 0.7242 1.6251
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.335612 0.104348 -12.800 <2e-16 ***
length 0.015516 0.000823 18.853 <2e-16 ***
differentTRUE 0.243892 0.126684 1.925 0.0542 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3358.2 on 2946 degrees of freedom
Residual deviance: 2427.3 on 2944 degrees of freedom
AIC: 2433.3
Number of Fisher Scoring iterations: 7