t-test: p=0.0096623
Neutral set average density: 6.75452e-05
Different set average density: 0.000153826
motif_present gene_set absent present different 952 42 neutral 1929 24
Fisher's exact test: p=5.63992e-07
Binomial GLM: p=1.01554e-06
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.2938 -0.2938 -0.1573 -0.1573 2.9662
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -4.3867 0.2054 -21.358 < 2e-16 ***
differentTRUE 1.2658 0.2589 4.889 1.02e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 631.96 on 2946 degrees of freedom
Residual deviance: 606.84 on 2945 degrees of freedom
AIC: 610.84
Number of Fisher Scoring iterations: 7
Binomial GLM adjusted for length: p=0.000330375
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.7354 -0.2388 -0.1551 -0.1339 3.1040
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -4.9385685 0.2529431 -19.524 < 2e-16 ***
length 0.0023952 0.0005212 4.596 4.32e-06 ***
differentTRUE 0.9643058 0.2685910 3.590 0.00033 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 631.96 on 2946 degrees of freedom
Residual deviance: 588.51 on 2944 degrees of freedom
AIC: 594.51
Number of Fisher Scoring iterations: 7