t-test: p=2.78203e-11
Neutral set average density: 0.0100709
Different set average density: 0.012243
motif_present gene_set absent present different 101 893 neutral 586 1367
Fisher's exact test: p=9.30249e-37
Binomial GLM: p=1.5556e-30
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.1385 0.4629 0.4629 0.8447 0.8447
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.84705 0.04938 17.16 <2e-16 ***
differentTRUE 1.33241 0.11601 11.49 <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: 3200.5 on 2946 degrees of freedom
Residual deviance: 3039.5 on 2945 degrees of freedom
AIC: 3043.5
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0116823
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.6512 0.0022 0.1913 0.6689 1.6350
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.3999180 0.1120369 -12.495 <2e-16 ***
length 0.0175279 0.0009447 18.554 <2e-16 ***
differentTRUE 0.3435291 0.1362346 2.522 0.0117 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3200.5 on 2946 degrees of freedom
Residual deviance: 2250.5 on 2944 degrees of freedom
AIC: 2256.5
Number of Fisher Scoring iterations: 7