createStandardMixes: Create Standard Mixes from a Matrix of Standard Compounds

In michaelwitting/MetaboAnnotation: Utilities for Annotation of Metabolomics Data

Create Standard Mixes from a Matrix of Standard Compounds

Description

The createStandardMixes function defines groups (mixes) of compounds (standards) with dissimilar m/z values. The expected size of the groups can be defined with parameters max_nstd and min_nstd and the minimum required difference between m/z values within each group with parameter min_diff. The group assignment will be reported in an additional column in the result data frame.

Usage

createStandardMixes(
  x,
  max_nstd = 10,
  min_nstd = 5,
  min_diff = 2,
  iterativeRandomization = FALSE
)

Arguments

x	numeric matrix with row names representing the compounds and columns representing different adducts. Such a matrix with m/z values for different adducts for compounds could e.g. be created with the MetaboCoreUtils::mass2mz() function.
max_nstd	numeric number of maximum standards per group.
min_nstd	numeric number of minimum standards per group. Only needed when using iterativeRandomization = TRUE.
min_diff	numeric Minimum difference for considering two values as distinct.
iterativeRandomization	logical default FALSE. If set to TRUE, createStandardMixes will randomly rearrange the rows of x until the user inputs are satisfied.

Details

Users should be aware that because the function iterates through x, the compounds at the bottom of the matrix are more complicated to group, and there is a possibility that some compounds will not be grouped with others. We advise specifyiong iterativeRandomization = TRUE even if it takes more time.

Value

data.frame created by adding a column group to the input x matrix, comprising the group number for each compound.

Author(s)

Philippine Louail

Examples

## Iterative grouping only
x <- matrix(c(135.0288, 157.0107, 184.0604, 206.0424, 265.1118, 287.0937,
              169.0356, 191.0176, 468.9809, 490.9628, 178.0532, 200.0352),
            ncol = 2, byrow = TRUE,
            dimnames = list(c("Malic Acid", "Pyridoxic Acid", "Thiamine",
                                "Uric acid", "dUTP", "N-Formyl-L-methionine"),
                             c("adduct_1", "adduct_2")))
result <- createStandardMixes(x, max_nstd = 3, min_diff = 2)

## Randomize grouping
set.seed(123)
x <- matrix(c(349.0544, 371.0363, 325.0431, 347.0251, 581.0416, 603.0235,
              167.0564, 189.0383, 150.0583, 172.0403, 171.0053, 192.9872,
              130.0863, 152.0682, 768.1225, 790.1044),
            ncol = 2, byrow = TRUE,
            dimnames = list(c("IMP", "UMP", "UDP-glucuronate",
                                "1-Methylxanthine", "Methionine",
                                "Dihydroxyacetone phosphate",
                                "Pipecolic acid", "CoA"),
                             c("[M+H]+", "[M+Na]+")))
result <- createStandardMixes(x, max_nstd = 4, min_nstd = 3, min_diff = 2,
                               iterativeRandomization = TRUE)

michaelwitting/MetaboAnnotation documentation built on Dec. 20, 2024, 5:34 a.m.