t-test: p=0.00289983
Neutral set average density: 0.0072174
Different set average density: 0.00810042
motif_present gene_set absent present different 201 793 neutral 790 1163
Fisher's exact test: p=2.37659e-29
Binomial GLM: p=4.25981e-27
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.7880 -1.3454 0.6722 1.0182 1.0182
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.38673 0.04610 8.388 <2e-16 ***
differentTRUE 0.98579 0.09144 10.780 <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: 3763.5 on 2946 degrees of freedom
Residual deviance: 3636.6 on 2945 degrees of freedom
AIC: 3640.6
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.319295
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.3325 -0.9104 0.2597 0.8541 1.6883
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.404094 0.091205 -15.395 <2e-16 ***
length 0.012091 0.000605 19.984 <2e-16 ***
differentTRUE 0.109442 0.109892 0.996 0.319
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3763.5 on 2946 degrees of freedom
Residual deviance: 2830.5 on 2944 degrees of freedom
AIC: 2836.5
Number of Fisher Scoring iterations: 6