molecularFormula2IPdb: Molecular Formula to IPDB

Description

A function to calculate IPDBs from a vector of molecular formulas

Usage

molecularFormula2IPdb(molecularFormulaDatabase, retentionTime = NULL, peak_spacing = 0,
intensity_cutoff_str = 1, IonPathways = "[M]+", number_processing_threads = 1,
UFA_IP_memeory_variables = c(1e30, 1e-12, 100), allowedMustRunCalculation = FALSE,
allowedVerbose = TRUE)

Value

An IPDB list of isotopic profiles

Arguments

molecularFormulaDatabase: A vector string of molecular formulas OR a list of elements and molecular formula matrix
retentionTime: retention time
peak_spacing: A maximum space between isotopologues in Da to merge neighboring isotopologues.
intensity_cutoff_str: A minimum intensity threshold for isotopic profiles in percentage. This parameter may be a string piece of R commands using c, b, br, cl, k, s, se, and si variables corresponding to the same elements.
IonPathways: A vector of ionization pathways. Pathways should be like [Coeff*M+ADD1-DED1+...] where "Coeff" should be an integer between 1-9 and ADD1 and DED1 may be ionization pathways. ex: 'IonPathways <- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")'
number_processing_threads: number of processing cores for multi-threaded computations.
UFA_IP_memeory_variables: A vector of three variables. Default values are c(1e30, 1e-12, 100) to manage memory usage. UFA_IP_memeory_variables[1] is used to control the overall size of isotopic combinations. UFA_IP_memeory_variables[2] indicates the minimum relative abundance (RA calculated by eq(1) in the reference [1]) of an isotopologue to include in the isotopic profile calculations. UFA_IP_memeory_variables[3] is the maximum elapsed time to calculate the isotopic profile on the `setTimeLimit` function of the base R.
allowedMustRunCalculation: c(TRUE, FALSE). A `TRUE` allowedMustRunCalculation applies a brute-force method to calculate complex isotopic profiles. When `TRUE`, this option may significantly reduce the speed for multithreaded processing.
allowedVerbose: c(TRUE, FALSE). A `TRUE` allowedVerbose provides messages about the flow of the function.

References

[1] Fakouri Baygi, S., Crimmins, B.S., Hopke, P.K. Holsen, T.M. (2016). Comprehensive emerging chemical discovery: novel polyfluorinated compounds in Lake Michigan trout. Environmental Science and Technology, 50(17), 9460-9468, tools:::Rd_expr_doi("10.1021/acs.est.6b01349").

Examples

Run this code

# \donttest{
library(IDSL.UFA, attach.required = TRUE)
molecular_formula <- c("C13F8N8O2", "C20H22", "C8HF16ClSO3", "C12Cl10", "C123H193N35O37")
peak_spacing <- 0.005 # in Da for QToF instruments
# Use this piece of code for intensity cutoff to preserve significant isotopologues
intensity_cutoff_str <- "if (s>0 & si>0) {min(c(c, 10, si*3, s*4))}
else if (s>0 & si==0) {min(c(c, 10, s*4))}
else if (s==0 & si>0) {min(c(c, 10, si*3))}
else if (s==0 & si==0) {min(c(c, 10))}"
UFA_IP_memeory_variables <- c(1e30, 1e-12, 100)
IonPathways <- c("[M+H]+", "[M+Na]+", "[M-H2O+H]+")
number_processing_threads <- 2
listIsoProDataBase <- molecularFormula2IPdb(molecular_formula, retentionTime = NULL,
peak_spacing, intensity_cutoff_str, IonPathways, number_processing_threads,
UFA_IP_memeory_variables, allowedMustRunCalculation = FALSE, allowedVerbose = TRUE)
save(listIsoProDataBase, file = "listIsoProDataBase.Rdata")
# }