t-test: p=0.421717
Neutral set average density: 7.7916e-06
Different set average density: 1.45007e-05
motif_present gene_set absent present different 987 7 neutral 1950 3
Fisher's exact test: p=0.0370808
Binomial GLM: p=0.027032
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.1189 -0.1189 -0.0554 -0.0554 3.5996
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -6.4770 0.5778 -11.210 <2e-16 ***
differentTRUE 1.5282 0.6912 2.211 0.027 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 133.69 on 2946 degrees of freedom
Residual deviance: 128.20 on 2945 degrees of freedom
AIC: 132.2
Number of Fisher Scoring iterations: 9
Binomial GLM adjusted for length: p=0.186917
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.5863 -0.0777 -0.0493 -0.0369 3.8269
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -7.728373 0.754738 -10.240 < 2e-16 ***
length 0.004369 0.001137 3.842 0.000122 ***
differentTRUE 0.938656 0.711235 1.320 0.186917
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 133.69 on 2946 degrees of freedom
Residual deviance: 115.61 on 2944 degrees of freedom
AIC: 121.61
Number of Fisher Scoring iterations: 9