t-test: p=0.864871
Neutral set average density: 1.56367e-05
Different set average density: 1.40261e-05
motif_present gene_set absent present different 988 6 neutral 1947 6
Fisher's exact test: p=0.235963
Binomial GLM: p=0.241076
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.1100 -0.1100 -0.0784 -0.0784 3.4016
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -5.7823 0.4089 -14.142 <2e-16 ***
differentTRUE 0.6784 0.5787 1.172 0.241
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 156.04 on 2946 degrees of freedom
Residual deviance: 154.69 on 2945 degrees of freedom
AIC: 158.69
Number of Fisher Scoring iterations: 8
Binomial GLM adjusted for length: p=0.66393
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.3705 -0.0925 -0.0726 -0.0621 3.5288
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -6.561443 0.547703 -11.980 < 2e-16 ***
length 0.003122 0.001100 2.838 0.00454 **
differentTRUE 0.261228 0.601225 0.434 0.66393
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 156.04 on 2946 degrees of freedom
Residual deviance: 148.09 on 2944 degrees of freedom
AIC: 154.09
Number of Fisher Scoring iterations: 8