t-test: p=7.73004e-29
Neutral set average density: 0.012226
Different set average density: 0.017451
motif_present gene_set absent present different 106 888 neutral 653 1300
Fisher's exact test: p=9.02151e-45
Binomial GLM: p=8.48301e-37
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.1158 -1.4802 0.4749 0.9022 0.9022
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.68854 0.04796 14.36 <2e-16 ***
differentTRUE 1.43699 0.11340 12.67 <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: 3362.4 on 2946 degrees of freedom
Residual deviance: 3163.8 on 2945 degrees of freedom
AIC: 3167.8
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0165023
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.5325 -0.6386 0.0983 0.5668 1.9208
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.207692 0.128984 -17.116 <2e-16 ***
length 0.023265 0.001135 20.499 <2e-16 ***
differentTRUE 0.339483 0.141592 2.398 0.0165 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3362.4 on 2946 degrees of freedom
Residual deviance: 2080.3 on 2944 degrees of freedom
AIC: 2086.3
Number of Fisher Scoring iterations: 7