t-test: p=4.22003e-05
Neutral set average density: 0.00113891
Different set average density: 0.000652051
motif_present gene_set absent present different 849 145 neutral 1711 242
Fisher's exact test: p=0.106175
Binomial GLM: p=0.0954502
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.5616 -0.5616 -0.5144 -0.5144 2.0436
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.95590 0.06868 -28.479 <2e-16 ***
differentTRUE 0.18857 0.11310 1.667 0.0955 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2292.1 on 2946 degrees of freedom
Residual deviance: 2289.4 on 2945 degrees of freedom
AIC: 2293.4
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.669496
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.1130 -0.5345 -0.4765 -0.4490 2.2051
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.3615814 0.0925472 -25.518 < 2e-16 ***
length 0.0019292 0.0002643 7.298 2.91e-13 ***
differentTRUE -0.0509268 0.1193110 -0.427 0.669
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 2292.1 on 2946 degrees of freedom
Residual deviance: 2239.8 on 2944 degrees of freedom
AIC: 2245.8
Number of Fisher Scoring iterations: 4