t-test: p=0.000105715
Neutral set average density: 0.0109205
Different set average density: 0.0122459
motif_present gene_set absent present different 90 904 neutral 529 1424
Fisher's exact test: p=6.68663e-33
Binomial GLM: p=2.70327e-27
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.1918 0.4357 0.4357 0.7948 0.7948
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.99024 0.05092 19.45 <2e-16 ***
differentTRUE 1.31678 0.12167 10.82 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3029.6 on 2946 degrees of freedom
Residual deviance: 2885.5 on 2945 degrees of freedom
AIC: 2889.5
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0290012
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.0146 0.0069 0.2033 0.6483 1.5691
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.242684 0.114554 -10.848 <2e-16 ***
length 0.017852 0.001002 17.821 <2e-16 ***
differentTRUE 0.309283 0.141647 2.183 0.029 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3029.6 on 2946 degrees of freedom
Residual deviance: 2157.9 on 2944 degrees of freedom
AIC: 2163.9
Number of Fisher Scoring iterations: 7