t-test: p=5.75093e-21
Neutral set average density: 0.0506138
Different set average density: 0.0581447
motif_present gene_set absent present different 10 984 neutral 69 1884
Fisher's exact test: p=2.91159e-05
Binomial GLM: p=0.000167588
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.0329 0.1422 0.2682 0.2682 0.2682
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 3.3070 0.1226 26.981 < 2e-16 ***
differentTRUE 1.2820 0.3406 3.763 0.000168 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 727.68 on 2946 degrees of freedom
Residual deviance: 708.75 on 2945 degrees of freedom
AIC: 712.75
Number of Fisher Scoring iterations: 7
Binomial GLM adjusted for length: p=0.865565
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.12938 0.00061 0.02724 0.17110 1.00339
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.536034 0.321125 -1.669 0.0951 .
length 0.048009 0.005345 8.982 <2e-16 ***
differentTRUE -0.062816 0.371046 -0.169 0.8656
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 727.68 on 2946 degrees of freedom
Residual deviance: 487.04 on 2944 degrees of freedom
AIC: 493.04
Number of Fisher Scoring iterations: 10