t-test: p=1.70962e-06
Neutral set average density: 0.00602866
Different set average density: 0.00722833
motif_present gene_set absent present different 213 781 neutral 879 1074
Fisher's exact test: p=1.43753e-37
Binomial GLM: p=1.62527e-34
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.7552 -1.2636 0.6945 1.0936 1.0936
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.20036 0.04548 4.405 1.06e-05 ***
differentTRUE 1.09892 0.08969 12.253 < 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: 3885.6 on 2946 degrees of freedom
Residual deviance: 3720.9 on 2945 degrees of freedom
AIC: 3724.9
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0262695
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.4883 -0.8608 0.2118 0.8150 1.7724
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.698968 0.093171 -18.235 <2e-16 ***
length 0.012456 0.000595 20.936 <2e-16 ***
differentTRUE 0.241356 0.108611 2.222 0.0263 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3885.6 on 2946 degrees of freedom
Residual deviance: 2823.1 on 2944 degrees of freedom
AIC: 2829.1
Number of Fisher Scoring iterations: 6