t-test: p=0.00881433
Neutral set average density: 0.0160504
Different set average density: 0.0149278
motif_present gene_set absent present different 61 933 neutral 330 1623
Fisher's exact test: p=1.15124e-17
Binomial GLM: p=5.77612e-15
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.3626 0.3559 0.6084 0.6084 0.6084
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.59294 0.06039 26.379 < 2e-16 ***
differentTRUE 1.13459 0.14530 7.809 5.78e-15 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2307.2 on 2946 degrees of freedom
Residual deviance: 2233.0 on 2945 degrees of freedom
AIC: 2237
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.257668
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.08056 0.05095 0.28244 0.62099 1.14025
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.224784 0.119549 -1.880 0.0601 .
length 0.014898 0.001079 13.806 <2e-16 ***
differentTRUE 0.181984 0.160775 1.132 0.2577
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2307.2 on 2946 degrees of freedom
Residual deviance: 1829.4 on 2944 degrees of freedom
AIC: 1835.4
Number of Fisher Scoring iterations: 7