MsCoreUtils: rla – R documentation

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rla

Calculate relative log abundances rla calculates the relative log abundances (RLA, see reference) on a numeric vector. rowRla performs row-wise RLA calculations on a numeric matrix.

Description

Calculate relative log abundances

rla calculates the relative log abundances (RLA, see reference) on a numeric vector. rowRla performs row-wise RLA calculations on a numeric matrix.

Usage

rla(
  x,
  f = rep_len(1, length(x)),
  transform = c("log2", "log10", "identity"),
  na.rm = TRUE
)

rowRla(x, f = rep_len(1, ncol(x)), transform = c("log2", "log10", "identity"))

Arguments

`x`	`numeric` (for `rla`) or `matrix` (for `rowRla`) with the abundances (in natural scale) on which the RLA should be calculated.
`f`	`factor`, `numeric` or `character` with the same length than `x` (or, for `rowRla` equal to the number of columns of `x`) allowing to define the grouping of values in `x`. If omitted all values are considered to be from the same group.
`transform`	`character(1)` defining the function to transform `x`. Defaults to `transform = "log2"` which `log2` transforms `x` prior to calculation. If `x` is already in log scale use `transform = "identity"` to avoid transformation of the values.
`na.rm`	`logical(1)` whether `NA` values should be removed prior to calculation of the group-wise medians.

Details

The RLA is defined as the (log2) abundance of an analyte relative to the median across all abundances of that analyte in samples of the same group. The grouping of values can be defined with parameter f.

Value

numeric with the relative log abundances (in log2 scale) with 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)

x <- rbind(c(324, 4542, 3422, 3232, 5432, 6535, 3321, 1121),
     c(12, 3341, 3034, 6540, 34, 4532, 56, 1221))
grp <- c("a", "b", "b", "b", "a", "b", "a", "b")

## row-wise RLA values
rowRla(x, grp)

MsCoreUtils

Core Utils for Mass Spectrometry Data

v1.2.0

Artistic-2.0

Authors

RforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut] (<https://orcid.org/0000-0002-1520-2268>), Johannes Rainer [aut] (<https://orcid.org/0000-0002-6977-7147>), Sebastian Gibb [aut] (<https://orcid.org/0000-0001-7406-4443>), Adriaan Sticker [ctb], Sigurdur Smarason [ctb], Thomas Naake [ctb]

Initial release

rla