t-test: p=6.33629e-08
Neutral set average density: 0.00451262
Different set average density: 0.00335601
motif_present gene_set absent present different 457 537 neutral 1069 884
Fisher's exact test: p=7.26838e-06
Binomial GLM: p=7.05109e-06
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.247 -1.098 -1.098 1.259 1.259
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.19002 0.04546 -4.180 2.92e-05 ***
differentTRUE 0.35134 0.07821 4.492 7.05e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4081.7 on 2946 degrees of freedom
Residual deviance: 4061.4 on 2945 degrees of freedom
AIC: 4065.4
Number of Fisher Scoring iterations: 3
Binomial GLM adjusted for length: p=0.0306593
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.6145 -0.9667 -0.8024 1.1502 1.6592
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.1099545 0.0691163 -16.059 <2e-16 ***
length 0.0050622 0.0002931 17.273 <2e-16 ***
differentTRUE -0.1932751 0.0894185 -2.161 0.0307 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4081.7 on 2946 degrees of freedom
Residual deviance: 3651.3 on 2944 degrees of freedom
AIC: 3657.3
Number of Fisher Scoring iterations: 4