t-test: p=0.261896
Neutral set average density: 0.00475815
Different set average density: 0.00499623
motif_present gene_set absent present different 317 677 neutral 964 989
Fisher's exact test: p=8.41746e-20
Binomial GLM: p=2.95556e-19
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.5118 -1.1883 0.8764 1.1666 1.1666
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.02560 0.04526 0.566 0.572
differentTRUE 0.73317 0.08173 8.970 <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: 4035.0 on 2946 degrees of freedom
Residual deviance: 3951.7 on 2945 degrees of freedom
AIC: 3955.7
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.462118
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.5818 -0.9079 0.2051 0.9450 1.7414
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.5116152 0.0821053 -18.411 <2e-16 ***
length 0.0093562 0.0004504 20.772 <2e-16 ***
differentTRUE -0.0731290 0.0994461 -0.735 0.462
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4035.0 on 2946 degrees of freedom
Residual deviance: 3171.2 on 2944 degrees of freedom
AIC: 3177.2
Number of Fisher Scoring iterations: 5