t-test: p=0.37756
Neutral set average density: 0.0370085
Different set average density: 0.0364379
motif_present gene_set absent present different 7 987 neutral 74 1879
Fisher's exact test: p=1.3891e-07
Binomial GLM: p=1.6001e-05
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.1483 0.1189 0.2779 0.2779 0.2779
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 3.2344 0.1185 27.291 < 2e-16 ***
differentTRUE 1.7143 0.3973 4.314 1.6e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 742.0 on 2946 degrees of freedom
Residual deviance: 712.9 on 2945 degrees of freedom
AIC: 716.9
Number of Fisher Scoring iterations: 7
Binomial GLM adjusted for length: p=0.292555
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.8334 0.0011 0.0336 0.1931 0.9688
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.352361 0.308607 -1.142 0.254
length 0.043253 0.004931 8.771 <2e-16 ***
differentTRUE 0.441896 0.419840 1.053 0.293
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 742.00 on 2946 degrees of freedom
Residual deviance: 510.34 on 2944 degrees of freedom
AIC: 516.34
Number of Fisher Scoring iterations: 10