contingencyCount {eudysbiome} | R Documentation |
Computes the frequencies of the contingency table as the cumulated microbial abundance difference classified into each condition and eubiotic/dysbiotic impact term for examining the significance of the association (contingency) between conditions and impacts by contingencyTest
.
contingencyCount(x, micro.anno=NULL, comp.anno=NULL)
x |
See |
micro.anno |
See |
comp.anno |
See |
Eubiotic impact is measured by variations of increased harmless and decreased harmful microbes, while the dysbiotic impact is measured by the decreased harmless and increased harmful microbes.
The frequencies of condition-impact terms in contingency table
data(microDiff) attach(microDiff) microCount = contingencyCount(x = data, micro.anno = micro.anno, comp.anno = comp.anno) detach(microDiff)