t-test: p=0.165163
Neutral set average density: 7.55687e-05
Different set average density: 4.12538e-05
motif_present gene_set absent present different 979 15 neutral 1931 22
Fisher's exact test: p=0.385132
Binomial GLM: p=0.379518
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.1744 -0.1744 -0.1505 -0.1505 2.9954
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -4.4748 0.2144 -20.870 <2e-16 ***
differentTRUE 0.2963 0.3371 0.879 0.38
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 397.48 on 2946 degrees of freedom
Residual deviance: 396.72 on 2945 degrees of freedom
AIC: 400.72
Number of Fisher Scoring iterations: 7
Binomial GLM adjusted for length: p=0.842137
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.5138 -0.1621 -0.1342 -0.1220 3.1712
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -5.1382828 0.2939463 -17.480 < 2e-16 ***
length 0.0027754 0.0006608 4.200 2.67e-05 ***
differentTRUE -0.0699932 0.3514409 -0.199 0.842
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 397.48 on 2946 degrees of freedom
Residual deviance: 382.07 on 2944 degrees of freedom
AIC: 388.07
Number of Fisher Scoring iterations: 7