unique_subformula_masses: unique_subformula_masses

In MetabolomicsBasics: Basic Functions to Investigate Metabolomics Data Matrices

unique_subformula_masses

Description

unique_subformula_masses will generate a numeric vector of potential sub formula masses regarding a chemical formula as input.

Usage

unique_subformula_masses(fml, names = TRUE, check_validity = FALSE)

Arguments

fml	Chemical formula.
names	Return respective sub formulas as vector names.
check_validity	Filter for chemically valid formulas.

Details

In mass spectrometry precursor masses are often fragmented and these fragments are recorded as MS^2 spectra. A frequent task is then to compute potential chemical formulas for the obtained MS^2 masses. The function unique_subformula_masses follows the reverse approach. It allows to calculate all masses that could be potential breakdown products of a precursor formula

Value

A named numeric vector. The names are the sub formulas for the calculated exact masses given as numeric.

Examples

# specify a formula and calculate all potential combinatorial masses
fml <- c("C6H12O6", "C11H16NO4PS", "C24H51O4P")[1]
tmp <- unique_subformula_masses(fml = fml)
length(tmp); any(duplicated(tmp))
hist(tmp, breaks=seq(floor(min(tmp))-1, ceiling(max(tmp))), main=fml)
# do the same as above but check for chemical plausibility
tmp2 <- unique_subformula_masses(fml = fml, check_validity=TRUE)
length(tmp2)
hist(tmp2, breaks=seq(floor(min(tmp2))-1, ceiling(max(tmp2))), main=fml)
mz <- 147
tmp[abs(tmp-mz)<0.5]
tmp2[abs(tmp2-mz)<0.5]

MetabolomicsBasics documentation built on May 29, 2024, 9:02 a.m.