t-test: p=0.0154589
Neutral set average density: 0.000203999
Different set average density: 0.000328624
motif_present gene_set absent present different 906 88 neutral 1875 78
Fisher's exact test: p=1.76438e-07
Binomial GLM: p=1.31351e-07
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4306 -0.4306 -0.2855 -0.2855 2.5379
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.1797 0.1156 -27.515 < 2e-16 ***
differentTRUE 0.8480 0.1607 5.277 1.31e-07 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1277.5 on 2946 degrees of freedom
Residual deviance: 1249.9 on 2945 degrees of freedom
AIC: 1253.9
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.00359201
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.1959 -0.3514 -0.2695 -0.2304 2.7534
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.870006 0.154008 -25.129 < 2e-16 ***
length 0.002923 0.000343 8.522 < 2e-16 ***
differentTRUE 0.490498 0.168444 2.912 0.00359 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1277.5 on 2946 degrees of freedom
Residual deviance: 1185.1 on 2944 degrees of freedom
AIC: 1191.1
Number of Fisher Scoring iterations: 6