t-test: p=0.923003
Neutral set average density: 0.012709
Different set average density: 0.0127476
motif_present gene_set absent present different 117 877 neutral 502 1451
Fisher's exact test: p=1.20648e-19
Binomial GLM: p=1.04849e-17
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.0686 0.5005 0.5005 0.7709 0.7709
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.06141 0.05178 20.498 <2e-16 ***
differentTRUE 0.95292 0.11121 8.568 <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: 3029.6 on 2946 degrees of freedom
Residual deviance: 2946.5 on 2945 degrees of freedom
AIC: 2950.5
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.566018
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.11603 0.01424 0.26013 0.71347 1.44611
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.9236516 0.1064858 -8.674 <2e-16 ***
length 0.0155544 0.0008925 17.427 <2e-16 ***
differentTRUE -0.0755527 0.1316420 -0.574 0.566
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3029.6 on 2946 degrees of freedom
Residual deviance: 2282.4 on 2944 degrees of freedom
AIC: 2288.4
Number of Fisher Scoring iterations: 7