t-test: p=0.12513
Neutral set average density: 0.0486931
Different set average density: 0.0475933
motif_present gene_set absent present different 6 988 neutral 49 1904
Fisher's exact test: p=0.000136381
Binomial GLM: p=0.000881577
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.1969 0.1100 0.2254 0.2254 0.2254
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 3.6599 0.1447 25.296 < 2e-16 ***
differentTRUE 1.4440 0.4342 3.326 0.000882 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 546.9 on 2946 degrees of freedom
Residual deviance: 531.2 on 2945 degrees of freedom
AIC: 535.2
Number of Fisher Scoring iterations: 7
Binomial GLM adjusted for length: p=0.767083
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.4059 0.0001 0.0096 0.1030 0.9985
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.872490 0.416219 -2.096 0.0361 *
length 0.062331 0.007887 7.903 2.73e-15 ***
differentTRUE 0.139113 0.469671 0.296 0.7671
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 546.9 on 2946 degrees of freedom
Residual deviance: 346.8 on 2944 degrees of freedom
AIC: 352.8
Number of Fisher Scoring iterations: 11