t-test: p=0.201276
Neutral set average density: 0.00557337
Different set average density: 0.00587343
motif_present gene_set absent present different 256 738 neutral 891 1062
Fisher's exact test: p=2.87602e-26
Binomial GLM: p=5.76474e-25
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.6471 -1.2528 0.7717 1.1038 1.1038
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.17556 0.04543 3.864 0.000111 ***
differentTRUE 0.88320 0.08559 10.319 < 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: 3939.5 on 2946 degrees of freedom
Residual deviance: 3826.5 on 2945 degrees of freedom
AIC: 3830.5
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.10315
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.5417 -0.9679 0.3278 0.9361 1.6525
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.2469363 0.0808340 -15.43 <2e-16 ***
length 0.0088172 0.0004559 19.34 <2e-16 ***
differentTRUE 0.1631954 0.1001340 1.63 0.103
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3939.5 on 2946 degrees of freedom
Residual deviance: 3165.8 on 2944 degrees of freedom
AIC: 3171.8
Number of Fisher Scoring iterations: 5