t-test: p=0.00211055
Neutral set average density: 0.00846792
Different set average density: 0.00753692
motif_present gene_set absent present different 210 784 neutral 685 1268
Fisher's exact test: p=2.61419e-15
Binomial GLM: p=1.29038e-14
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.7633 -1.4475 0.6889 0.9294 0.9294
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.61578 0.04742 12.986 < 2e-16 ***
differentTRUE 0.70152 0.09103 7.707 1.29e-14 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3618.7 on 2946 degrees of freedom
Residual deviance: 3555.8 on 2945 degrees of freedom
AIC: 3559.8
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.670715
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.8912 -1.0719 0.4325 0.9040 1.4029
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.7087705 0.0815424 -8.692 <2e-16 ***
length 0.0087607 0.0005051 17.343 <2e-16 ***
differentTRUE -0.0448338 0.1054500 -0.425 0.671
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3618.7 on 2946 degrees of freedom
Residual deviance: 3022.2 on 2944 degrees of freedom
AIC: 3028.2
Number of Fisher Scoring iterations: 6