t-test: p=9.67716e-08
Neutral set average density: 0.00439404
Different set average density: 0.00555593
motif_present gene_set absent present different 285 709 neutral 1034 919
Fisher's exact test: p=9.43834e-37
Binomial GLM: p=6.67435e-35
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.581 -1.128 0.822 1.228 1.228
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.11790 0.04533 -2.601 0.0093 **
differentTRUE 1.02927 0.08351 12.325 <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: 4053.0 on 2946 degrees of freedom
Residual deviance: 3891.8 on 2945 degrees of freedom
AIC: 3895.8
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0174758
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.6886 -0.8348 0.1292 0.8738 1.8504
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.8851326 0.0886831 -21.257 <2e-16 ***
length 0.0106325 0.0004892 21.734 <2e-16 ***
differentTRUE 0.2414570 0.1016002 2.377 0.0175 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4053.0 on 2946 degrees of freedom
Residual deviance: 2989.5 on 2944 degrees of freedom
AIC: 2995.5
Number of Fisher Scoring iterations: 5