t-test: p=0.09813
Neutral set average density: 0.00418445
Different set average density: 0.00453531
motif_present gene_set absent present different 355 639 neutral 1064 889
Fisher's exact test: p=4.16784e-22
Binomial GLM: p=1.19132e-21
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.435 -1.102 0.940 1.255 1.255
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.17969 0.04544 -3.955 7.67e-05 ***
differentTRUE 0.76748 0.08029 9.559 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4081.4 on 2946 degrees of freedom
Residual deviance: 3987.4 on 2945 degrees of freedom
AIC: 3991.4
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.893943
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.2304 -0.8682 0.0959 0.9219 1.8542
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.7291523 0.0825827 -20.938 <2e-16 ***
length 0.0090267 0.0004221 21.386 <2e-16 ***
differentTRUE -0.0130557 0.0979299 -0.133 0.894
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4081.4 on 2946 degrees of freedom
Residual deviance: 3176.8 on 2944 degrees of freedom
AIC: 3182.8
Number of Fisher Scoring iterations: 5