getDenom {ALDEx2} | R Documentation

## getDenom

### Description

Returns the denominator used as the basis for the log-ratio, for an `aldex.clr` object.

### Usage

    getDenom(.object)

### Arguments

`.object` | A `aldex.clr` object containing the Monte Carlo Dirochlet instances derived from estimating the technical variance of the raw read count data, along with sample and feature information.

### Details

Returns the denominator used to calculate the log-ratios. "all" is the centred log-ratio. "iqlr" is the interquartile log-ratio. A vector of numbers is the offset of the variables used in the denominator

### Value

A vector of values.

### See Also

`aldex.clr`

### Examples

    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 = "iqlr", verbose = FALSE)
    Denom <- getDenom(x)

    # to find the names of housekeeping genes used
    getFeatureNames(x)[getDenom(x)]

[Package ALDEx2 version 1.22.0 Index]