t-test: p=2.93397e-17
Neutral set average density: 0.108529
Different set average density: 0.0948283
motif_present gene_set absent present different 3 991 neutral 17 1936
Fisher's exact test: p=0.0960876
Binomial GLM: p=0.0896342
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.4068 0.0778 0.1322 0.1322 0.1322
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 4.7352 0.2436 19.438 <2e-16 ***
differentTRUE 1.0649 0.6274 1.697 0.0896 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 239.58 on 2946 degrees of freedom
Residual deviance: 235.95 on 2945 degrees of freedom
AIC: 239.95
Number of Fisher Scoring iterations: 8
Binomial GLM adjusted for length: p=0.701396
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.3987 0.0000 0.0049 0.0572 0.7294
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.10642 0.65338 0.163 0.871
length 0.06666 0.01335 4.995 5.89e-07 ***
differentTRUE -0.25129 0.65536 -0.383 0.701
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 239.58 on 2946 degrees of freedom
Residual deviance: 162.11 on 2944 degrees of freedom
AIC: 168.11
Number of Fisher Scoring iterations: 12