t-test: p=1.85265e-10
Neutral set average density: 0.0176516
Different set average density: 0.0204269
motif_present gene_set absent present different 45 949 neutral 353 1600
Fisher's exact test: p=6.18849e-28
Binomial GLM: p=5.25107e-21
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.4880 0.3044 0.6314 0.6314 0.6314
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.5113 0.0588 25.701 <2e-16 ***
differentTRUE 1.5375 0.1635 9.404 <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: 2333.3 on 2946 degrees of freedom
Residual deviance: 2212.2 on 2945 degrees of freedom
AIC: 2216.2
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.0349854
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.4969 0.0062 0.1300 0.5019 1.5093
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.269285 0.148206 -8.564 <2e-16 ***
length 0.025808 0.001614 15.993 <2e-16 ***
differentTRUE 0.394796 0.187238 2.109 0.035 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2333.3 on 2946 degrees of freedom
Residual deviance: 1573.5 on 2944 degrees of freedom
AIC: 1579.5
Number of Fisher Scoring iterations: 8