t-test: p=0.0572752
Neutral set average density: 0.000250259
Different set average density: 0.000337999
motif_present gene_set absent present different 885 109 neutral 1838 115
Fisher's exact test: p=1.55157e-06
Binomial GLM: p=1.26907e-06
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4820 -0.4820 -0.3484 -0.3484 2.3800
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.77150 0.09612 -28.833 < 2e-16 ***
differentTRUE 0.67726 0.13980 4.845 1.27e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1585.0 on 2946 degrees of freedom
Residual deviance: 1561.9 on 2945 degrees of freedom
AIC: 1565.9
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.244386
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.7339 -0.3745 -0.2858 -0.2443 2.6893
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.836460 0.141638 -27.086 <2e-16 ***
length 0.004195 0.000309 13.577 <2e-16 ***
differentTRUE 0.175783 0.151004 1.164 0.244
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1585.0 on 2946 degrees of freedom
Residual deviance: 1383.4 on 2944 degrees of freedom
AIC: 1389.4
Number of Fisher Scoring iterations: 6