t-test: p=0.936257
Neutral set average density: 0.000379474
Different set average density: 0.000373573
motif_present gene_set absent present different 908 86 neutral 1855 98
Fisher's exact test: p=0.000194744
Binomial GLM: p=0.00013871
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4254 -0.4254 -0.3209 -0.3209 2.4463
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.9407 0.1036 -28.37 < 2e-16 ***
differentTRUE 0.5838 0.1532 3.81 0.000139 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1377.0 on 2946 degrees of freedom
Residual deviance: 1362.7 on 2945 degrees of freedom
AIC: 1366.7
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.186783
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.9656 -0.3627 -0.2925 -0.2580 2.6673
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.6382129 0.1414611 -25.719 <2e-16 ***
length 0.0029694 0.0003285 9.039 <2e-16 ***
differentTRUE 0.2132556 0.1615382 1.320 0.187
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1377.0 on 2946 degrees of freedom
Residual deviance: 1289.8 on 2944 degrees of freedom
AIC: 1295.8
Number of Fisher Scoring iterations: 6