t-test: p=8.58019e-13
Neutral set average density: 0.00425002
Different set average density: 0.00578603
motif_present gene_set absent present different 286 708 neutral 1035 918
Fisher's exact test: p=1.58331e-36
Binomial GLM: p=9.14198e-35
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.5784 -1.1269 0.8238 1.2288 1.2288
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.11996 0.04534 -2.646 0.00815 **
differentTRUE 1.02641 0.08345 12.299 < 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: 4053.8 on 2946 degrees of freedom
Residual deviance: 3893.4 on 2945 degrees of freedom
AIC: 3897.4
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.200079
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.0394 -0.7855 0.0840 0.7992 1.9782
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.1537986 0.0952967 -22.601 <2e-16 ***
length 0.0124841 0.0005499 22.702 <2e-16 ***
differentTRUE 0.1350050 0.1053634 1.281 0.2
---
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: 2831.0 on 2944 degrees of freedom
AIC: 2837
Number of Fisher Scoring iterations: 6