construction: Consensus structural classifications for putative ionisation...

In jasenfinch/construction: Consensus Structural Chemical Classifications for Putative Molecular Formula Assignments

Consensus structural classifications for putative ionisation products

Description

Perform consensus structural classification for molecular formulas assigned to m/z features from electrospray ionisation mass spectrometry approaches.

Usage

construction(
  x,
  library_path = tempdir(),
  db = "kegg",
  organism = character(),
  threshold = 66,
  adduct_rules_table = adduct_rules(),
  classyfireR_cache = NULL
)

## S4 method for signature 'tbl_df'
construction(
  x,
  library_path = paste0(tempdir(), "/construction_library"),
  db = "kegg",
  organism = character(),
  threshold = 66,
  adduct_rules_table = adduct_rules(),
  classyfireR_cache = NULL
)

## S4 method for signature 'Assignment'
construction(
  x,
  library_path = tempdir(),
  db = "kegg",
  organism = character(),
  threshold = 66,
  classyfireR_cache = NULL
)

Arguments

x	The molecular formulas and adducts to search. This should either be a tibble containing two character columns named MF and Adduct or and S4 object of class Assignment.
library_path	the target file path for the classification library in which to store consensus classification data
db	the databases to search. This can either be kegg and/or pubchem.
organism	the KEGG organism ID. This is Ignored if argument db is set to pubchem
threshold	the percentage majority threshold for consensus classification
adduct_rules_table	a data frame containing the adduct formation rules. The defaults is mzAnnotation::adduct_rules().
classyfireR_cache	the file path for a classyfireR cache. See the documentation of classyfireR::get_classification for more details.

Value

If argument x is a tibble, then a tibble is returned containing the consensus structural classifications. If argument x is an object of S4 class Assignment, and object of S4 class Construction is returned.

Examples

x <- tibble::tibble(MF = c('C12H22O11','C4H6O5'),
                    Adduct = c('[M+Cl]1-','[M-H]1-'))
structural_classifications <- construction(x)

structural_classifications

jasenfinch/construction documentation built on Sept. 2, 2023, 8:14 a.m.