t-test: p=0.439391
Neutral set average density: 0.00348303
Different set average density: 0.00363714
motif_present gene_set absent present different 418 576 neutral 1194 759
Fisher's exact test: p=9.03768e-23
Binomial GLM: p=1.66576e-22
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.316 -0.992 -0.992 1.375 1.375
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.45306 0.04642 -9.76 <2e-16 ***
differentTRUE 0.77369 0.07927 9.76 <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: 4059.3 on 2946 degrees of freedom
Residual deviance: 3962.5 on 2945 degrees of freedom
AIC: 3966.5
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.233023
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.8393 -0.8377 -0.6445 0.9477 1.8816
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.8114196 0.0797258 -22.721 <2e-16 ***
length 0.0073517 0.0003524 20.860 <2e-16 ***
differentTRUE 0.1120628 0.0939646 1.193 0.233
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4059.3 on 2946 degrees of freedom
Residual deviance: 3269.2 on 2944 degrees of freedom
AIC: 3275.2
Number of Fisher Scoring iterations: 5