t-test: p=2.34076e-23
Neutral set average density: 0.00322069
Different set average density: 0.0014572
motif_present gene_set absent present different 693 301 neutral 1289 664
Fisher's exact test: p=0.0420714
Binomial GLM: p=0.0421538
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.9116 -0.9116 -0.8494 1.4689 1.5457
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.66334 0.04777 -13.887 <2e-16 ***
differentTRUE -0.17058 0.08395 -2.032 0.0422 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3727.1 on 2946 degrees of freedom
Residual deviance: 3723.0 on 2945 degrees of freedom
AIC: 3727
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=7.54417e-09
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.8812 -0.8504 -0.7655 1.2875 1.9248
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.2196933 0.0667464 -18.274 < 2e-16 ***
length 0.0028364 0.0002284 12.418 < 2e-16 ***
differentTRUE -0.5330016 0.0922413 -5.778 7.54e-09 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3727.1 on 2946 degrees of freedom
Residual deviance: 3556.8 on 2944 degrees of freedom
AIC: 3562.8
Number of Fisher Scoring iterations: 4