t-test: p=0.232635
Neutral set average density: 0.0119059
Different set average density: 0.01239
motif_present gene_set absent present different 135 859 neutral 595 1358
Fisher's exact test: p=3.05415e-25
Binomial GLM: p=1.36123e-22
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.9982 0.5403 0.5403 0.8525 0.8525
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.82521 0.04916 16.785 <2e-16 ***
differentTRUE 1.02529 0.10483 9.781 <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: 3299.5 on 2946 degrees of freedom
Residual deviance: 3191.1 on 2945 degrees of freedom
AIC: 3195.1
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.525974
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.2405 0.0026 0.2728 0.7648 1.5017
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.0578994 0.0996542 -10.616 <2e-16 ***
length 0.0139883 0.0007703 18.160 <2e-16 ***
differentTRUE 0.0783285 0.1235145 0.634 0.526
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3299.5 on 2946 degrees of freedom
Residual deviance: 2492.7 on 2944 degrees of freedom
AIC: 2498.7
Number of Fisher Scoring iterations: 6