t-test: p=1.66657e-29
Neutral set average density: 0.030021
Different set average density: 0.0231903
motif_present gene_set absent present different 21 973 neutral 45 1908
Fisher's exact test: p=0.793494
Binomial GLM: p=0.739868
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.7775 0.2067 0.2159 0.2159 0.2159
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 3.74715 0.15082 24.846 <2e-16 ***
differentTRUE 0.08871 0.26719 0.332 0.74
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 631.96 on 2946 degrees of freedom
Residual deviance: 631.85 on 2945 degrees of freedom
AIC: 635.85
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.00688775
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.1692 0.0781 0.1769 0.2642 0.5523
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 2.340972 0.236398 9.903 < 2e-16 ***
length 0.011730 0.002037 5.757 8.54e-09 ***
differentTRUE -0.772461 0.285861 -2.702 0.00689 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 631.96 on 2946 degrees of freedom
Residual deviance: 568.94 on 2944 degrees of freedom
AIC: 574.94
Number of Fisher Scoring iterations: 8