t-test: p=0.0190473
Neutral set average density: 0.00748337
Different set average density: 0.00680567
motif_present gene_set absent present different 276 718 neutral 792 1161
Fisher's exact test: p=6.63235e-12
Binomial GLM: p=1.13498e-11
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.6008 -1.3436 0.8066 1.0199 1.0199
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.38248 0.04609 8.299 < 2e-16 ***
differentTRUE 0.57359 0.08450 6.788 1.13e-11 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3859.3 on 2946 degrees of freedom
Residual deviance: 3811.7 on 2945 degrees of freedom
AIC: 3815.7
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=6.24663e-05
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.3313 -0.9405 0.2695 0.9035 1.7535
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.3559850 0.0874189 -15.511 < 2e-16 ***
length 0.0116566 0.0005639 20.673 < 2e-16 ***
differentTRUE -0.4290630 0.1071775 -4.003 6.25e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3859.3 on 2946 degrees of freedom
Residual deviance: 2959.5 on 2944 degrees of freedom
AIC: 2965.5
Number of Fisher Scoring iterations: 6