t-test: p=0.840835
Neutral set average density: 0.0131719
Different set average density: 0.0132474
motif_present gene_set absent present different 70 924 neutral 413 1540
Fisher's exact test: p=5.90333e-25
Binomial GLM: p=1.28419e-20
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.3036 0.3822 0.6893 0.6893 0.6893
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.31609 0.05541 23.75 <2e-16 ***
differentTRUE 1.26413 0.13579 9.31 <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: 2629.2 on 2946 degrees of freedom
Residual deviance: 2521.5 on 2945 degrees of freedom
AIC: 2525.5
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.0247691
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.6369 0.0364 0.2827 0.6600 1.2749
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.5363790 0.1125257 -4.767 1.87e-06 ***
length 0.0147707 0.0009777 15.107 < 2e-16 ***
differentTRUE 0.3391847 0.1510855 2.245 0.0248 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2629.2 on 2946 degrees of freedom
Residual deviance: 2036.1 on 2944 degrees of freedom
AIC: 2042.1
Number of Fisher Scoring iterations: 7