t-test: p=3.48563e-29
Neutral set average density: 0.00998147
Different set average density: 0.0141419
motif_present gene_set absent present different 121 873 neutral 691 1262
Fisher's exact test: p=3.77985e-44
Binomial GLM: p=4.09926e-37
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.0523 -1.4415 0.5095 0.9345 0.9345
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.60231 0.04732 12.73 <2e-16 ***
differentTRUE 1.37383 0.10793 12.73 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3469.7 on 2946 degrees of freedom
Residual deviance: 3274.3 on 2945 degrees of freedom
AIC: 3278.3
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0614995
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.1910 -0.6741 0.0911 0.5845 1.9271
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.30550 0.12750 -18.08 <2e-16 ***
length 0.02291 0.00109 21.02 <2e-16 ***
differentTRUE 0.25644 0.13714 1.87 0.0615 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3469.7 on 2946 degrees of freedom
Residual deviance: 2130.7 on 2944 degrees of freedom
AIC: 2136.7
Number of Fisher Scoring iterations: 7