t-test: p=2.19693e-81
Neutral set average density: 0.156564
Different set average density: 0.194747
motif_present gene_set absent present different 0 994 neutral 4 1949
Fisher's exact test: p=0.30719
Binomial GLM: p=0.991452
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.519 0.000 0.064 0.064 0.064
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 6.1888 0.5005 12.365 <2e-16 ***
differentTRUE 16.3773 1528.6889 0.011 0.991
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 60.813 on 2946 degrees of freedom
Residual deviance: 57.518 on 2945 degrees of freedom
AIC: 61.518
Number of Fisher Scoring iterations: 21
Binomial GLM adjusted for length: p=0.994398
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.6127 0.0000 0.0001 0.0129 0.3873
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 8.624e-01 1.483e+00 0.582 0.5608
length 8.451e-02 3.504e-02 2.412 0.0159 *
differentTRUE 1.594e+01 2.271e+03 0.007 0.9944
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 60.813 on 2946 degrees of freedom
Residual deviance: 41.704 on 2944 degrees of freedom
AIC: 47.704
Number of Fisher Scoring iterations: 23