t-test: p=2.35894e-06
Neutral set average density: 0.0131366
Different set average density: 0.0149156
motif_present gene_set absent present different 72 922 neutral 445 1508
Fisher's exact test: p=1.35809e-28
Binomial GLM: p=2.76007e-23
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.2913 0.3878 0.7191 0.7191 0.7191
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.22047 0.05395 22.623 <2e-16 ***
differentTRUE 1.32941 0.13373 9.941 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2737.2 on 2946 degrees of freedom
Residual deviance: 2612.9 on 2945 degrees of freedom
AIC: 2616.9
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.154688
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.8522 0.0070 0.1723 0.5793 1.5507
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.27273 0.12792 -9.949 <2e-16 ***
length 0.02139 0.00124 17.241 <2e-16 ***
differentTRUE 0.22280 0.15655 1.423 0.155
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2737.2 on 2946 degrees of freedom
Residual deviance: 1898.0 on 2944 degrees of freedom
AIC: 1904
Number of Fisher Scoring iterations: 7