t-test: p=0.0028581
Neutral set average density: 0.00474346
Different set average density: 0.00548285
motif_present gene_set absent present different 280 714 neutral 966 987
Fisher's exact test: p=4.96853e-29
Binomial GLM: p=9.7137e-28
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.5918 -1.1866 0.8135 1.1683 1.1683
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.02151 0.04526 0.475 0.635
differentTRUE 0.91459 0.08379 10.916 <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: 4014.9 on 2946 degrees of freedom
Residual deviance: 3889.2 on 2945 degrees of freedom
AIC: 3893.2
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=6.53753e-06
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.0751 -1.0096 0.4419 1.0357 1.5359
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.957964 0.071827 -13.337 < 2e-16 ***
length 0.005607 0.000338 16.588 < 2e-16 ***
differentTRUE 0.417821 0.092680 4.508 6.54e-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: 3488.2 on 2944 degrees of freedom
AIC: 3494.2
Number of Fisher Scoring iterations: 5