t-test: p=0.294227
Neutral set average density: 0.000344782
Different set average density: 0.000410464
motif_present gene_set absent present different 884 110 neutral 1824 129
Fisher's exact test: p=4.36592e-05
Binomial GLM: p=3.30372e-05
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4843 -0.4843 -0.3697 -0.3697 2.3312
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.64897 0.09111 -29.076 < 2e-16 ***
differentTRUE 0.56500 0.13610 4.151 3.3e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1658.8 on 2946 degrees of freedom
Residual deviance: 1642.0 on 2945 degrees of freedom
AIC: 1646
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.305563
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.4679 -0.4050 -0.3233 -0.2846 2.5900
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.4576033 0.1279777 -27.017 <2e-16 ***
length 0.0033903 0.0002989 11.343 <2e-16 ***
differentTRUE 0.1485713 0.1450074 1.025 0.306
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1658.8 on 2946 degrees of freedom
Residual deviance: 1522.7 on 2944 degrees of freedom
AIC: 1528.7
Number of Fisher Scoring iterations: 5