t-test: p=0.611997
Neutral set average density: 0.000205557
Different set average density: 0.000230733
motif_present gene_set absent present different 941 53 neutral 1887 66
Fisher's exact test: p=0.0131451
Binomial GLM: p=0.0115802
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.3310 -0.3310 -0.2622 -0.2622 2.6029
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.3531 0.1252 -26.776 <2e-16 ***
differentTRUE 0.4764 0.1887 2.525 0.0116 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 996.97 on 2946 degrees of freedom
Residual deviance: 990.75 on 2945 degrees of freedom
AIC: 994.75
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.159795
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.6207 -0.3033 -0.2617 -0.2384 2.7081
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.6918612 0.1625221 -22.716 < 2e-16 ***
length 0.0015929 0.0004308 3.698 0.000218 ***
differentTRUE 0.2775209 0.1974167 1.406 0.159795
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 996.97 on 2946 degrees of freedom
Residual deviance: 978.52 on 2944 degrees of freedom
AIC: 984.52
Number of Fisher Scoring iterations: 6