t-test: p=0.693263
Neutral set average density: 0.0240944
Different set average density: 0.0238781
motif_present gene_set absent present different 50 944 neutral 231 1722
Fisher's exact test: p=7.01434e-10
Binomial GLM: p=8.07871e-09
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.4453 0.3213 0.5018 0.5018 0.5018
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 2.00882 0.07007 28.669 < 2e-16 ***
differentTRUE 0.92928 0.16114 5.767 8.08e-09 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1855.1 on 2946 degrees of freedom
Residual deviance: 1816.2 on 2945 degrees of freedom
AIC: 1820.2
Number of Fisher Scoring iterations: 5
Binomial GLM adjusted for length: p=0.214813
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.0448 0.0279 0.1972 0.5040 1.1496
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.216567 0.145968 -1.484 0.138
length 0.020330 0.001544 13.168 <2e-16 ***
differentTRUE -0.225864 0.182084 -1.240 0.215
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1855.1 on 2946 degrees of freedom
Residual deviance: 1419.5 on 2944 degrees of freedom
AIC: 1425.5
Number of Fisher Scoring iterations: 8