t-test: p=7.03708e-06
Neutral set average density: 0.0223052
Different set average density: 0.0244902
motif_present gene_set absent present different 38 956 neutral 278 1675
Fisher's exact test: p=2.03724e-20
Binomial GLM: p=8.58058e-16
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.5551 0.2792 0.5542 0.5542 0.5542
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.79595 0.06476 27.731 < 2e-16 ***
differentTRUE 1.42922 0.17764 8.046 8.58e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2008.0 on 2946 degrees of freedom
Residual deviance: 1920.9 on 2945 degrees of freedom
AIC: 1924.9
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.528889
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.9107 0.0022 0.0753 0.3902 1.5564
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.543297 0.177433 -8.698 <2e-16 ***
length 0.034290 0.002207 15.537 <2e-16 ***
differentTRUE 0.132636 0.210632 0.630 0.529
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2008.0 on 2946 degrees of freedom
Residual deviance: 1275.2 on 2944 degrees of freedom
AIC: 1281.2
Number of Fisher Scoring iterations: 8