t-test: p=2.40985e-10
Neutral set average density: 0.0116223
Different set average density: 0.00825294
motif_present gene_set absent present different 362 632 neutral 884 1069
Fisher's exact test: p=4.68344e-06
Binomial GLM: p=4.51355e-06
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.4213 -1.2591 0.9517 1.0979 1.0979
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.19002 0.04546 4.180 2.92e-05 ***
differentTRUE 0.36722 0.08007 4.586 4.51e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4014.9 on 2946 degrees of freedom
Residual deviance: 3993.6 on 2945 degrees of freedom
AIC: 3997.6
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=3.66489e-06
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.7057 -0.9808 0.3046 1.0193 1.7369
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.1497596 0.0768886 -14.95 < 2e-16 ***
length 0.0082458 0.0004172 19.77 < 2e-16 ***
differentTRUE -0.4549671 0.0982749 -4.63 3.66e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4014.9 on 2946 degrees of freedom
Residual deviance: 3321.9 on 2944 degrees of freedom
AIC: 3327.9
Number of Fisher Scoring iterations: 5