matchFormula: Chemical Formula Matching

In michaelwitting/MetaboAnnotation: Utilities for Annotation of Metabolomics Data

Chemical Formula Matching

Description

The matchFormula method matches chemical formulas from different inputs (parameter query and target). Before comparison all formulas are normalized using MetaboCoreUtils::standardizeFormula(). Inputs can be either a character or data.frame containing a column with formulas. In case of data.frames parameter formulaColname needs to be used to specify the name of the column containing the chemical formulas.

Usage

matchFormula(query, target, ...)

## S4 method for signature 'character,character'
matchFormula(query, target, BPPARAM = SerialParam())

## S4 method for signature 'data.frameOrSimilar,data.frameOrSimilar'
matchFormula(
  query,
  target,
  formulaColname = c("formula", "formula"),
  BPPARAM = SerialParam()
)

## S4 method for signature 'character,data.frameOrSimilar'
matchFormula(
  query,
  target,
  formulaColname = "formula",
  BPPARAM = SerialParam()
)

## S4 method for signature 'data.frameOrSimilar,character'
matchFormula(
  query,
  target,
  formulaColname = "formula",
  BPPARAM = SerialParam()
)

Arguments

query	character or data.frame with chemical formulas to search.
target	character or data.frame with chemical formulas to compare against.
...	currently ignored
BPPARAM	parallel processing setup. See BiocParallel::bpparam() for details.
formulaColname	character with the name of the column containing chemical formulas. Can be of length 1 if both query and target are data.frames and the name of the column with chemical formulas is the same for both. If different columns are used, formulaColname[1] can be used to define the column name in query and formulaColname[2] the one of target.

Value

Matched object representing the result.

Author(s)

Michael Witting

Examples

## input formula
query <- c("H12C6O6", "C11H12O2", "HN3")
target <- c("HCl", "C2H4O", "C6H12O6")

query_df <- data.frame(
    formula = c("H12C6O6", "C11H12O2", "HN3"),
    name = c("A", "B", "C")
)
target_df <- data.frame(
    formula = c("HCl", "C2H4O", "C6H12O6"),
    name = c("D", "E", "F")
)

## character vs character
matches <- matchFormula(query, target)
matchedData(matches)

## data.frame vs data.frame
matches <- matchFormula(query_df, target_df)
matchedData(matches)
## data.frame vs character
matches <- matchFormula(query_df, target)
matchedData(matches)
## character vs data.frame
matches <- matchFormula(query, target_df)
matchedData(matches)

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