t-test: p=0.00102459
Neutral set average density: 0.0188351
Different set average density: 0.0173278
motif_present gene_set absent present different 36 958 neutral 256 1697
Fisher's exact test: p=2.80913e-18
Binomial GLM: p=2.64537e-14
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.5761 0.2716 0.5301 0.5301 0.5301
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.89144 0.06705 28.210 < 2e-16 ***
differentTRUE 1.38989 0.18253 7.615 2.65e-14 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1904.1 on 2946 degrees of freedom
Residual deviance: 1826.8 on 2945 degrees of freedom
AIC: 1830.8
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.015067
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.1641 0.0579 0.2597 0.5483 0.9999
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.141139 0.132612 1.064 0.2872
length 0.014589 0.001239 11.773 <2e-16 ***
differentTRUE 0.474262 0.195108 2.431 0.0151 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1904.1 on 2946 degrees of freedom
Residual deviance: 1536.5 on 2944 degrees of freedom
AIC: 1542.5
Number of Fisher Scoring iterations: 7