rla: Calculate relative log abundances 'rla' calculates the...
In MsCoreUtils: Core Utils for Mass Spectrometry Data

Description Usage Arguments Details Value Author(s) References Examples

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.

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"))

`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.

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.

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).

Johannes Rainer

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.

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)