t-test: p=3.72571e-10
Neutral set average density: 0.0221553
Different set average density: 0.0252462
motif_present gene_set absent present different 29 965 neutral 268 1685
Fisher's exact test: p=1.06094e-23
Binomial GLM: p=6.95336e-17
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.6587 0.2434 0.5433 0.5433 0.5433
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.83853 0.06576 27.957 <2e-16 ***
differentTRUE 1.66630 0.19961 8.348 <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: 1926.1 on 2946 degrees of freedom
Residual deviance: 1824.1 on 2945 degrees of freedom
AIC: 1828.1
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.0171977
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.0285 0.0074 0.1186 0.4489 1.3149
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.936120 0.163381 -5.730 1.01e-08 ***
length 0.026891 0.001903 14.133 < 2e-16 ***
differentTRUE 0.525669 0.220642 2.382 0.0172 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1926.1 on 2946 degrees of freedom
Residual deviance: 1330.4 on 2944 degrees of freedom
AIC: 1336.4
Number of Fisher Scoring iterations: 8