generate_connectivity_matrix: Generate connectivity matrices

In szymczak-lab/preprocessHighResMS: Preprocessing of spectra data from high resolution mass spectrometry

Description

Generates matrices summarizing connections between adducts and isotopes.

Usage

generate_connectivity_matrix(
  info.features,
  type,
  ids.use = NULL,
  ratios = FALSE
)

Arguments

info.features	data.frame with information about theoretical possible features (e.g. as generated by the function chem_formula_2_adducts).
type	Character. Type of connectivity matrix to generate ("adducts", "isotopes").
ids.use	Character vector. Feature identifiers to be used for connectivity matrix. If NULL connectivity matrix is build using all features in info.features.
ratios	Logical. Should the isotope connectivity matrix contain the expected abundance ratios? (deafult = TRUE).

Value

matrix with theoretical possible features in rows and columns. In the adduct matrix, the cell i,j contains 1, if features i and j are monoisotopic isotopes and adducts of the same chemical formula and 0 otherwise. In the isotope matrix, the cell i,j contains 1, if features i and j are isotopes of the same adduct (or the ratio of the theoretical abundances if ratios = TRUE) and 0 otherwise.

Examples

data("info.features")

add.m = generate_connectivity_matrix(info.features = info.features,
                                     type = "adducts")

iso.m = generate_connectivity_matrix(info.features = info.features,
                                     type = "isotopes")

szymczak-lab/preprocessHighResMS documentation built on Oct. 6, 2020, 12:50 a.m.