t-test: p=0.798125
Neutral set average density: 0.00369219
Different set average density: 0.00364006
motif_present gene_set absent present different 425 569 neutral 1166 787
Fisher's exact test: p=3.19882e-18
Binomial GLM: p=4.27623e-18
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.304 -1.016 -1.016 1.348 1.348
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.39311 0.04613 -8.521 <2e-16 ***
differentTRUE 0.68490 0.07899 8.671 <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: 4066.7 on 2946 degrees of freedom
Residual deviance: 3990.5 on 2945 degrees of freedom
AIC: 3994.5
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.352283
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.7135 -0.8912 -0.7018 1.0397 1.8067
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.5598169 0.0752177 -20.74 <2e-16 ***
length 0.0063147 0.0003239 19.50 <2e-16 ***
differentTRUE 0.0851806 0.0915753 0.93 0.352
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4066.7 on 2946 degrees of freedom
Residual deviance: 3423.9 on 2944 degrees of freedom
AIC: 3429.9
Number of Fisher Scoring iterations: 4