contingencyCount: Contingency Table Construction

In eudysbiome: Cartesian plot and contingency test on 16S Microbial data

Description

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.

Usage

contingencyCount(x, micro.anno=NULL, comp.anno=NULL)

Arguments

x	See x in Cartesian, the x values should be difference values without log converted.
micro.anno	See micro.anno in Cartesian.
comp.anno	See comp.anno in Cartesian.

Details

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.

Value

The frequencies of condition-impact terms in contingency table

Examples

data(microDiff)
attach(microDiff)

microCount = contingencyCount(x = data, micro.anno = micro.anno,
                      comp.anno = comp.anno)

detach(microDiff)

Example output

eudysbiome documentation built on Nov. 8, 2020, 7:49 p.m.