t-test: p=0.000228963
Neutral set average density: 0.00862117
Different set average density: 0.00970262
motif_present gene_set absent present different 118 876 neutral 654 1299
Fisher's exact test: p=8.75265e-40
Binomial GLM: p=1.37052e-33
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.0645 -1.4792 0.5027 0.9031 0.9031
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.68624 0.04795 14.31 <2e-16 ***
differentTRUE 1.31844 0.10916 12.08 <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: 3389.6 on 2946 degrees of freedom
Residual deviance: 3214.7 on 2945 degrees of freedom
AIC: 3218.7
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.00270455
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.9302 -0.8306 0.2070 0.7127 1.6770
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.4425461 0.1058728 -13.625 <2e-16 ***
length 0.0158780 0.0008337 19.045 <2e-16 ***
differentTRUE 0.3846792 0.1282493 2.999 0.0027 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3389.6 on 2946 degrees of freedom
Residual deviance: 2407.5 on 2944 degrees of freedom
AIC: 2413.5
Number of Fisher Scoring iterations: 7