t-test: p=0.700284
Neutral set average density: 0.000515758
Different set average density: 0.000545314
motif_present gene_set absent present different 853 141 neutral 1775 178
Fisher's exact test: p=4.30803e-05
Binomial GLM: p=3.20834e-05
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.5531 -0.5531 -0.4372 -0.4372 2.1888
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.29977 0.07862 -29.251 < 2e-16 ***
differentTRUE 0.49977 0.12019 4.158 3.21e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2020.7 on 2946 degrees of freedom
Residual deviance: 2003.7 on 2945 degrees of freedom
AIC: 2007.7
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.946449
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.8881 -0.4485 -0.3510 -0.3073 2.5433
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.3240585 0.1172261 -28.356 <2e-16 ***
length 0.0042111 0.0002815 14.959 <2e-16 ***
differentTRUE -0.0088492 0.1317510 -0.067 0.946
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2020.7 on 2946 degrees of freedom
Residual deviance: 1777.4 on 2944 degrees of freedom
AIC: 1783.4
Number of Fisher Scoring iterations: 5