t-test: p=2.08195e-30
Neutral set average density: 0.0080041
Different set average density: 0.0119953
motif_present gene_set absent present different 140 854 neutral 790 1163
Fisher's exact test: p=5.19878e-52
Binomial GLM: p=5.26742e-44
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.980 -1.345 0.551 1.018 1.018
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.3867 0.0461 8.388 <2e-16 ***
differentTRUE 1.4216 0.1022 13.913 <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: 3674.8 on 2946 degrees of freedom
Residual deviance: 3443.9 on 2945 degrees of freedom
AIC: 3447.9
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.000212346
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.6693 -0.7326 0.1242 0.6530 1.9010
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.1407409 0.1138152 -18.809 < 2e-16 ***
length 0.0183294 0.0008637 21.221 < 2e-16 ***
differentTRUE 0.4652949 0.1256244 3.704 0.000212 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3674.8 on 2946 degrees of freedom
Residual deviance: 2367.6 on 2944 degrees of freedom
AIC: 2373.6
Number of Fisher Scoring iterations: 7