t-test: p=0.46596
Neutral set average density: 0.000173454
Different set average density: 0.000208045
motif_present gene_set absent present different 947 47 neutral 1901 52
Fisher's exact test: p=0.00468174
Binomial GLM: p=0.00368623
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.3113 -0.3113 -0.2323 -0.2323 2.6929
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.5989 0.1406 -25.604 < 2e-16 ***
differentTRUE 0.5957 0.2052 2.904 0.00369 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 866.53 on 2946 degrees of freedom
Residual deviance: 858.29 on 2945 degrees of freedom
AIC: 862.29
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=0.0443597
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.5300 -0.2847 -0.2333 -0.2154 2.7765
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.8753516 0.1791943 -21.627 < 2e-16 ***
length 0.0013252 0.0004807 2.757 0.00584 **
differentTRUE 0.4315144 0.2146117 2.011 0.04436 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 866.53 on 2946 degrees of freedom
Residual deviance: 851.40 on 2944 degrees of freedom
AIC: 857.4
Number of Fisher Scoring iterations: 6