t-test: p=0.841988
Neutral set average density: 0.00092291
Different set average density: 0.000943625
motif_present gene_set absent present different 786 208 neutral 1668 285
Fisher's exact test: p=1.80377e-05
Binomial GLM: p=1.46342e-05
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.6853 -0.6853 -0.5617 -0.5617 1.9620
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.7669 0.0641 -27.566 < 2e-16 ***
differentTRUE 0.4375 0.1009 4.334 1.46e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2661.5 on 2946 degrees of freedom
Residual deviance: 2643.0 on 2945 degrees of freedom
AIC: 2647
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.449556
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.6900 -0.5877 -0.4924 -0.4472 2.2119
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.4183190 0.0893633 -27.062 <2e-16 ***
length 0.0029807 0.0002463 12.102 <2e-16 ***
differentTRUE 0.0818447 0.1082380 0.756 0.45
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2661.5 on 2946 degrees of freedom
Residual deviance: 2498.6 on 2944 degrees of freedom
AIC: 2504.6
Number of Fisher Scoring iterations: 4