t-test: p=3.04741e-34
Neutral set average density: 0.0086974
Different set average density: 0.0126715
motif_present gene_set absent present different 125 869 neutral 745 1208
Fisher's exact test: p=3.34642e-51
Binomial GLM: p=1.31095e-42
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.0364 -1.3883 0.5184 0.9802 0.9802
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.48334 0.04658 10.38 <2e-16 ***
differentTRUE 1.45569 0.10640 13.68 <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: 3576.2 on 2946 degrees of freedom
Residual deviance: 3348.5 on 2945 degrees of freedom
AIC: 3352.5
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.00221742
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-5.5478 -0.6743 0.0874 0.5922 1.9694
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.40083 0.12582 -19.082 < 2e-16 ***
length 0.02203 0.00103 21.384 < 2e-16 ***
differentTRUE 0.41063 0.13422 3.059 0.00222 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3576.2 on 2946 degrees of freedom
Residual deviance: 2175.8 on 2944 degrees of freedom
AIC: 2181.8
Number of Fisher Scoring iterations: 7