t-test: p=0.697104
Neutral set average density: 0.0144663
Different set average density: 0.0143092
motif_present gene_set absent present different 53 941 neutral 379 1574
Fisher's exact test: p=1.07531e-27
Binomial GLM: p=1.46311e-21
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.4213 0.3310 0.6569 0.6569 0.6569
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.42384 0.05722 24.885 <2e-16 ***
differentTRUE 1.45281 0.15233 9.538 <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: 2456.3 on 2946 degrees of freedom
Residual deviance: 2335.8 on 2945 degrees of freedom
AIC: 2339.8
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.000110343
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.9414 0.0663 0.3095 0.6425 1.1436
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.1812279 0.1111077 -1.631 0.10287
length 0.0124382 0.0009269 13.420 < 2e-16 ***
differentTRUE 0.6337730 0.1639077 3.867 0.00011 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2456.3 on 2946 degrees of freedom
Residual deviance: 1973.0 on 2944 degrees of freedom
AIC: 1979
Number of Fisher Scoring iterations: 7