contingencyCount {eudysbiome} | R Documentation

## 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`.

### 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)

[Package eudysbiome version 1.12.0 Index]