Calculate relative log abundances — rla • MsCoreUtils

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.

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).

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.

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.

Author

Johannes Rainer

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)
#> [1] -0.4150375  0.0000000  0.3219281 -1.0000000  0.0000000  0.5849625 -0.1926451
#> [8]  0.0000000  0.1699250

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)
#>           [,1]      [,2]       [,3]        [,4]      [,5]      [,6]      [,7]
#> [1,] -3.357552 0.4084879  0.0000000 -0.08241256 0.7098658 0.9333475 0.0000000
#> [2,] -1.502500 0.0000000 -0.1390589  0.96901065 0.0000000 0.4398679 0.7198921
#>           [,8]
#> [1,] -1.610053
#> [2,] -1.452217