t-test: p=1.0932e-11
Neutral set average density: 0.0134205
Different set average density: 0.0094177
motif_present gene_set absent present different 323 671 neutral 825 1128
Fisher's exact test: p=3.05964e-07
Binomial GLM: p=3.11936e-07
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.4994 -1.3128 0.8865 1.0478 1.0478
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.31282 0.04581 6.828 8.58e-12 ***
differentTRUE 0.41830 0.08176 5.116 3.12e-07 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3940.4 on 2946 degrees of freedom
Residual deviance: 3913.8 on 2945 degrees of freedom
AIC: 3917.8
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=8.12723e-06
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.9319 -0.9925 0.3321 0.9793 1.7404
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.1160899 0.0794462 -14.048 < 2e-16 ***
length 0.0091003 0.0004602 19.773 < 2e-16 ***
differentTRUE -0.4502497 0.1009120 -4.462 8.13e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3940.4 on 2946 degrees of freedom
Residual deviance: 3211.5 on 2944 degrees of freedom
AIC: 3217.5
Number of Fisher Scoring iterations: 5