t-test: p=0.251961
Neutral set average density: 0.00939865
Different set average density: 0.0090472
motif_present gene_set absent present different 176 818 neutral 613 1340
Fisher's exact test: p=6.00682e-16
Binomial GLM: p=4.89658e-15
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.8608 -1.5223 0.6243 0.8680 0.8680
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.78206 0.04876 16.04 < 2e-16 ***
differentTRUE 0.75432 0.09634 7.83 4.9e-15 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3424.3 on 2946 degrees of freedom
Residual deviance: 3358.4 on 2945 degrees of freedom
AIC: 3362.4
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0847648
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.2265 -0.9694 0.3136 0.8126 1.5015
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.9485004 0.0931629 -10.181 <2e-16 ***
length 0.0124962 0.0006794 18.392 <2e-16 ***
differentTRUE -0.1997591 0.1158908 -1.724 0.0848 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3424.3 on 2946 degrees of freedom
Residual deviance: 2669.9 on 2944 degrees of freedom
AIC: 2675.9
Number of Fisher Scoring iterations: 6