t-test: p=0.40383
Neutral set average density: 0.000213268
Different set average density: 0.00024836
motif_present gene_set absent present different 916 78 neutral 1868 85
Fisher's exact test: p=0.000159117
Binomial GLM: p=0.000108428
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4043 -0.4043 -0.2983 -0.2983 2.5038
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.0900 0.1109 -27.865 < 2e-16 ***
differentTRUE 0.6267 0.1619 3.871 0.000108 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1260.5 on 2946 degrees of freedom
Residual deviance: 1245.8 on 2945 degrees of freedom
AIC: 1249.8
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.275777
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.3293 -0.3342 -0.2604 -0.2259 2.7574
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.9586686 0.1556683 -25.43 <2e-16 ***
length 0.0035200 0.0003394 10.37 <2e-16 ***
differentTRUE 0.1869951 0.1715780 1.09 0.276
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1260.5 on 2946 degrees of freedom
Residual deviance: 1148.9 on 2944 degrees of freedom
AIC: 1154.9
Number of Fisher Scoring iterations: 6