t-test: p=0.15622
Neutral set average density: 0.000102833
Different set average density: 6.51413e-05
motif_present gene_set absent present different 967 27 neutral 1914 39
Fisher's exact test: p=0.236006
Binomial GLM: p=0.213863
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.2347 -0.2347 -0.2009 -0.2009 2.7977
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.8934 0.1617 -24.072 <2e-16 ***
differentTRUE 0.3150 0.2534 1.243 0.214
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 631.96 on 2946 degrees of freedom
Residual deviance: 630.45 on 2945 degrees of freedom
AIC: 634.45
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.496959
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.9017 -0.2058 -0.1632 -0.1448 3.0753
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -4.8533810 0.2343823 -20.707 < 2e-16 ***
length 0.0037100 0.0004808 7.716 1.2e-14 ***
differentTRUE -0.1810586 0.2665439 -0.679 0.497
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 631.96 on 2946 degrees of freedom
Residual deviance: 579.97 on 2944 degrees of freedom
AIC: 585.97
Number of Fisher Scoring iterations: 7