t-test: p=0.0791196
Neutral set average density: 0.00518634
Different set average density: 0.00477671
motif_present gene_set absent present different 348 646 neutral 973 980
Fisher's exact test: p=1.89666e-14
Binomial GLM: p=2.92556e-14
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.4488 -1.1805 0.9284 1.1744 1.1744
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.007168 0.045257 0.158 0.874
differentTRUE 0.611429 0.080434 7.602 2.93e-14 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4053.8 on 2946 degrees of freedom
Residual deviance: 3994.7 on 2945 degrees of freedom
AIC: 3998.7
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.259629
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.1908 -0.9521 0.2582 1.0152 1.7061
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.2981656 0.0767479 -16.915 <2e-16 ***
length 0.0077272 0.0003924 19.694 <2e-16 ***
differentTRUE -0.1078700 0.0956916 -1.127 0.26
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4053.8 on 2946 degrees of freedom
Residual deviance: 3349.8 on 2944 degrees of freedom
AIC: 3355.8
Number of Fisher Scoring iterations: 5