eudysbiome (version 1.2.0)

contingencyCount: Contingency Table Construction

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.

Value

The frequencies of condition-impact terms in contingency table

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.

Examples

data(microDiff)
attach(microDiff)

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

detach(microDiff)