t-test: p=0.0442318
Neutral set average density: 0.00434816
Different set average density: 0.00484232
motif_present gene_set absent present different 336 658 neutral 1058 895
Fisher's exact test: p=5.77826e-26
Binomial GLM: p=3.57563e-25
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.4728 -1.1072 0.9083 1.2492 1.2492
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.16731 0.04541 -3.684 0.00023 ***
differentTRUE 0.83941 0.08098 10.365 < 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: 4076.8 on 2946 degrees of freedom
Residual deviance: 3965.6 on 2945 degrees of freedom
AIC: 3969.6
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=5.70347e-07
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.6132 -0.9979 0.4458 1.0923 1.5549
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.9383016 0.0680457 -13.789 < 2e-16 ***
length 0.0042029 0.0002822 14.893 < 2e-16 ***
differentTRUE 0.4398309 0.0879486 5.001 5.7e-07 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4076.8 on 2946 degrees of freedom
Residual deviance: 3678.7 on 2944 degrees of freedom
AIC: 3684.7
Number of Fisher Scoring iterations: 4