t-test: p=0.00150603
Neutral set average density: 0.000108614
Different set average density: 0.000237999
motif_present gene_set absent present different 931 63 neutral 1915 38
Fisher's exact test: p=2.57971e-09
Binomial GLM: p=4.54689e-09
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.3619 -0.3619 -0.1982 -0.1982 2.8070
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.9199 0.1638 -23.929 < 2e-16 ***
differentTRUE 1.2268 0.2092 5.863 4.55e-09 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 879.93 on 2946 degrees of freedom
Residual deviance: 844.16 on 2945 degrees of freedom
AIC: 848.16
Number of Fisher Scoring iterations: 6
Binomial GLM adjusted for length: p=9.60831e-06
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.8169 -0.2992 -0.1955 -0.1722 2.9322
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -4.4011777 0.2019446 -21.794 < 2e-16 ***
length 0.0021462 0.0004404 4.874 1.10e-06 ***
differentTRUE 0.9616752 0.2172882 4.426 9.61e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 879.93 on 2946 degrees of freedom
Residual deviance: 823.18 on 2944 degrees of freedom
AIC: 829.18
Number of Fisher Scoring iterations: 6