t-test: p=0.710271
Neutral set average density: 0.000401853
Different set average density: 0.000380122
motif_present gene_set absent present different 882 112 neutral 1802 151
Fisher's exact test: p=0.00204822
Binomial GLM: p=0.00154623
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4890 -0.4890 -0.4012 -0.4012 2.2627
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.47937 0.08472 -29.266 < 2e-16 ***
differentTRUE 0.41568 0.13130 3.166 0.00155 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1772.8 on 2946 degrees of freedom
Residual deviance: 1763.0 on 2945 degrees of freedom
AIC: 1767
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.597308
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.6591 -0.4122 -0.3263 -0.2890 2.5838
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.4354049 0.1242506 -27.649 <2e-16 ***
length 0.0039248 0.0002923 13.429 <2e-16 ***
differentTRUE -0.0752478 0.1424404 -0.528 0.597
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1772.8 on 2946 degrees of freedom
Residual deviance: 1589.1 on 2944 degrees of freedom
AIC: 1595.1
Number of Fisher Scoring iterations: 5