t-test: p=0.688053
Neutral set average density: 3.65134e-05
Different set average density: 4.61022e-05
motif_present gene_set absent present different 984 10 neutral 1938 15
Fisher's exact test: p=0.527269
Binomial GLM: p=0.506677
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.1422 -0.1422 -0.1242 -0.1242 3.1206
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -4.8614 0.2592 -18.757 <2e-16 ***
differentTRUE 0.2723 0.4101 0.664 0.507
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 288.27 on 2946 degrees of freedom
Residual deviance: 287.84 on 2945 degrees of freedom
AIC: 291.84
Number of Fisher Scoring iterations: 7
Binomial GLM adjusted for length: p=0.742984
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4692 -0.1314 -0.1071 -0.0967 3.3408
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -5.6248392 0.3617567 -15.549 < 2e-16 ***
length 0.0030861 0.0007756 3.979 6.92e-05 ***
differentTRUE -0.1399607 0.4268341 -0.328 0.743
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 288.27 on 2946 degrees of freedom
Residual deviance: 274.86 on 2944 degrees of freedom
AIC: 280.86
Number of Fisher Scoring iterations: 8