t-test: p=7.79139e-06
Neutral set average density: 0.0280406
Different set average density: 0.0255305
motif_present gene_set absent present different 17 977 neutral 155 1798
Fisher's exact test: p=1.18329e-13
Binomial GLM: p=6.01428e-10
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.8525 0.1857 0.4067 0.4067 0.4067
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 2.45101 0.08371 29.28 < 2e-16 ***
differentTRUE 1.60027 0.25852 6.19 6.01e-10 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1311.1 on 2946 degrees of freedom
Residual deviance: 1254.8 on 2945 degrees of freedom
AIC: 1258.8
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.247537
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.5527 0.0019 0.0541 0.2936 1.2571
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.997124 0.223574 -4.460 8.2e-06 ***
length 0.038657 0.003183 12.146 < 2e-16 ***
differentTRUE 0.331635 0.286794 1.156 0.248
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1311.08 on 2946 degrees of freedom
Residual deviance: 864.79 on 2944 degrees of freedom
AIC: 870.79
Number of Fisher Scoring iterations: 9