aldex.set.mode {ALDEx2} | R Documentation

## identify set of denominator features for log-ratio calculation

### Description

calculate the features that are to be used as the denominator for the Geometric Mean calculation in clr_function.R

### Usage

    aldex.set.mode(reads, conds, denom="all")

### Arguments

`reads` | A data frame containing the samples and features per sample.
`conds` | A vector describing which samples belong to what condition.
`denom` | Character argument specifying which indicies to return. 'all' returns all features in both conditons. 'zero' returns the nonzero count features per condition. 'iqlr' returns the features whose variance falls within the inter-quantile range of the CLR-transformed data. In cases of malformed or null queries, input defaults to 'all'. Additionally, the input can be a numeric vector, which contains a set of row indicies to center the data against. Only for advanced users who can pre-determine the invariant set of features within their data.

### Details

An explicit example for two conditions is shown in the ‘Examples’ below.

### Value

Outputs a vector containing indicies per condition.

### Author(s)

Jia Rong Wu

### References

Please use the citation given by `citation(package="ALDEx")`.

### See Also

`aldex.clr`, `aldex.ttest`, `aldex.effect`, `selex`

### Examples

        # x is the output of the \code{x <- clr(data, mc.samples)} function
        # conditions is a description of the data
        # for the selex dataset, conditions <- c(rep("N", 7), rep("S", 7))
        # input can be "all", "iqlr", "zero" or numeric for advanced users
        data(selex)
        #subset for efficiency
        selex <- selex[1201:1600,]
        conds <- c(rep("NS", 7), rep("S", 7))
        x <- aldex.clr(selex, conds, mc.samples=2, denom="all")

[Package ALDEx2 version 1.20.0 Index]