t-test: p=5.49347e-14
Neutral set average density: 0.00798066
Different set average density: 0.0101964
motif_present gene_set absent present different 142 852 neutral 696 1257
Fisher's exact test: p=2.73813e-36
Binomial GLM: p=7.41556e-32
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.9728 -1.4365 0.5553 0.9388 0.9388
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.59113 0.04725 12.51 <2e-16 ***
differentTRUE 1.20063 0.10222 11.75 <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: 3518.8 on 2946 degrees of freedom
Residual deviance: 3359.3 on 2945 degrees of freedom
AIC: 3363.3
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0155698
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.4050 -0.8741 0.2363 0.7653 1.6243
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.3939407 0.0998284 -13.963 <2e-16 ***
length 0.0142898 0.0007408 19.290 <2e-16 ***
differentTRUE 0.2921654 0.1207870 2.419 0.0156 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3518.8 on 2946 degrees of freedom
Residual deviance: 2560.6 on 2944 degrees of freedom
AIC: 2566.6
Number of Fisher Scoring iterations: 6