t-test: p=0.0124539
Neutral set average density: 0.00633573
Different set average density: 0.00696344
motif_present gene_set absent present different 220 774 neutral 831 1122
Fisher's exact test: p=8.42151e-29
Binomial GLM: p=5.72226e-27
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.7367 -1.3073 0.7073 1.0529 1.0529
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.30024 0.04577 6.56 5.38e-11 ***
differentTRUE 0.95771 0.08906 10.75 < 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: 3839.7 on 2946 degrees of freedom
Residual deviance: 3714.7 on 2945 degrees of freedom
AIC: 3718.7
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.905901
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.3142 -0.8728 0.2071 0.8236 1.7767
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.6495857 0.0942007 -17.511 <2e-16 ***
length 0.0131446 0.0006262 20.990 <2e-16 ***
differentTRUE 0.0130268 0.1101995 0.118 0.906
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3839.7 on 2946 degrees of freedom
Residual deviance: 2791.5 on 2944 degrees of freedom
AIC: 2797.5
Number of Fisher Scoring iterations: 6