t-test: p=5.1549e-35
Neutral set average density: 0.0538961
Different set average density: 0.0646088
motif_present gene_set absent present different 5 989 neutral 81 1872
Fisher's exact test: p=7.74827e-10
Binomial GLM: p=3.44708e-06
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.2534 0.1004 0.2911 0.2911 0.2911
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 3.1403 0.1135 27.671 < 2e-16 ***
differentTRUE 2.1469 0.4625 4.642 3.45e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 777.35 on 2946 degrees of freedom
Residual deviance: 737.08 on 2945 degrees of freedom
AIC: 741.08
Number of Fisher Scoring iterations: 8
Binomial GLM adjusted for length: p=0.0552635
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.5303 0.0002 0.0167 0.1524 1.1660
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.051898 0.332734 -3.161 0.00157 **
length 0.053938 0.005759 9.365 < 2e-16 ***
differentTRUE 0.938915 0.489835 1.917 0.05526 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 777.35 on 2946 degrees of freedom
Residual deviance: 491.25 on 2944 degrees of freedom
AIC: 497.25
Number of Fisher Scoring iterations: 10