t-test: p=0.458033
Neutral set average density: 0.0523891
Different set average density: 0.0519033
motif_present gene_set absent present different 1 993 neutral 15 1938
Fisher's exact test: p=0.0168651
Binomial GLM: p=0.0484541
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.7153 0.0449 0.1242 0.1242 0.1242
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 4.8614 0.2592 18.756 <2e-16 ***
differentTRUE 2.0394 1.0334 1.973 0.0485 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 198.82 on 2946 degrees of freedom
Residual deviance: 191.76 on 2945 degrees of freedom
AIC: 195.76
Number of Fisher Scoring iterations: 9
Binomial GLM adjusted for length: p=0.466339
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.0083 0.0001 0.0067 0.0629 0.5554
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.62457 0.69500 0.899 0.369
length 0.05833 0.01354 4.308 1.65e-05 ***
differentTRUE 0.76330 1.04784 0.728 0.466
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 198.82 on 2946 degrees of freedom
Residual deviance: 141.58 on 2944 degrees of freedom
AIC: 147.58
Number of Fisher Scoring iterations: 12