t-test: p=3.12616e-05
Neutral set average density: 0.0346399
Different set average density: 0.0321085
motif_present gene_set absent present different 15 979 neutral 76 1877
Fisher's exact test: p=0.000271251
Binomial GLM: p=0.000657899
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.8961 0.1744 0.2818 0.2818 0.2818
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 3.2067 0.1170 27.406 < 2e-16 ***
differentTRUE 0.9718 0.2853 3.407 0.000658 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 812.10 on 2946 degrees of freedom
Residual deviance: 798.04 on 2945 degrees of freedom
AIC: 802.04
Number of Fisher Scoring iterations: 7
Binomial GLM adjusted for length: p=0.258455
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-4.0860 0.0047 0.0692 0.2488 0.9667
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.195560 0.264039 0.741 0.459
length 0.033546 0.003746 8.955 <2e-16 ***
differentTRUE -0.348193 0.308122 -1.130 0.258
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 812.1 on 2946 degrees of freedom
Residual deviance: 597.9 on 2944 degrees of freedom
AIC: 603.9
Number of Fisher Scoring iterations: 9