t-test: p=2.08873e-08
Neutral set average density: 0.00361575
Different set average density: 0.0021404
motif_present gene_set absent present different 707 287 neutral 1446 507
Fisher's exact test: p=0.0952692
Binomial GLM: p=0.0920705
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.8255 -0.7753 -0.7753 1.5762 1.6423
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.04805 0.05161 -20.306 <2e-16 ***
differentTRUE 0.14650 0.08696 1.685 0.0921 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3434.4 on 2946 degrees of freedom
Residual deviance: 3431.5 on 2945 degrees of freedom
AIC: 3435.5
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.000101045
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.1636 -0.7195 -0.6072 0.7816 2.1125
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.9396150 0.0770514 -25.173 < 2e-16 ***
length 0.0042994 0.0002523 17.042 < 2e-16 ***
differentTRUE -0.3845002 0.0988923 -3.888 0.000101 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3434.4 on 2946 degrees of freedom
Residual deviance: 3090.2 on 2944 degrees of freedom
AIC: 3096.2
Number of Fisher Scoring iterations: 4