t-test: p=0.118455
Neutral set average density: 0.000167845
Different set average density: 0.000107738
motif_present gene_set absent present different 958 36 neutral 1904 49
Fisher's exact test: p=0.102652
Binomial GLM: p=0.0896671
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.2716 -0.2716 -0.2254 -0.2254 2.7149
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.6599 0.1447 -25.296 <2e-16 ***
differentTRUE 0.3786 0.2231 1.697 0.0897 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 770.33 on 2946 degrees of freedom
Residual deviance: 767.51 on 2945 degrees of freedom
AIC: 771.51
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.9004
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.8609 -0.2434 -0.1973 -0.1769 2.9401
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -4.4177973 0.2009245 -21.987 < 2e-16 ***
length 0.0031131 0.0004432 7.024 2.15e-12 ***
differentTRUE -0.0292901 0.2340292 -0.125 0.9
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 770.33 on 2946 degrees of freedom
Residual deviance: 725.54 on 2944 degrees of freedom
AIC: 731.54
Number of Fisher Scoring iterations: 6