t-test: p=0.00629744
Neutral set average density: 0.0337135
Different set average density: 0.0355535
motif_present gene_set absent present different 9 985 neutral 98 1855
Fisher's exact test: p=8.95474e-10
Binomial GLM: p=5.55456e-07
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.0674 0.1349 0.3209 0.3209 0.3209
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 2.9407 0.1036 28.371 < 2e-16 ***
differentTRUE 1.7547 0.3505 5.006 5.55e-07 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 919.63 on 2946 degrees of freedom
Residual deviance: 880.06 on 2945 degrees of freedom
AIC: 884.06
Number of Fisher Scoring iterations: 7
Binomial GLM adjusted for length: p=0.187507
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.4060 0.0012 0.0388 0.2170 1.0943
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.654076 0.275968 -2.370 0.0178 *
length 0.042635 0.004287 9.945 <2e-16 ***
differentTRUE 0.494512 0.375202 1.318 0.1875
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 919.63 on 2946 degrees of freedom
Residual deviance: 617.96 on 2944 degrees of freedom
AIC: 623.96
Number of Fisher Scoring iterations: 10