rla {xcms} | R Documentation

## Calculate relative log abundances `rla` calculates the relative log abundances (RLA, see reference) on a `numeric` vector.

### Description

Calculate relative log abundances

`rla` calculates the relative log abundances (RLA, see reference) on a `numeric` vector.

`rowRla` calculates row-wise RLAs.

### Usage

    rla(x, group, log.transform = TRUE)

    rowRla(x, group, log.transform = TRUE)

### Arguments

`x` | `numeric` (for `rla`) or `matrix` (for `rowRla`) with the abundances (in natural scale) on which the RLA should be calculated.
`group` | `factor`, `numeric` or `character` with the same length than `x` that groups values in `x`. If omitted all values are considered to be from the same group.
`log.transform` | `logical(1)` whether `x` should be log2 transformed. Set to `log.transform = FALSE` if `x` is already in log scale.

### Details

The RLA is defines as the (log) abundance of an analyte relative to the median across all abundances of the same group.

### Value

`numeric` of the same length than `x` (for `rla`) or `matrix` with the same dimensions than `x` (for `rowRla`).

### Author(s)

Johannes Rainer

### References

De Livera AM, Dias DA, De Souza D, Rupasinghe T, Pyke J, Tull D, Roessner U, McConville M, Speed TP. Normalizing and integrating metabolomics data. Anal Chem 2012 Dec 18;84(24):10768-76.

### Examples

    x <- c(3, 4, 5, 1, 2, 3, 7, 8, 9)

    grp <- c(1, 1, 1, 2, 2, 2, 3, 3, 3)

    rla(x, grp)

[Package xcms version 3.6.2 Index]