Description Usage Arguments Value Examples
View source: R/annotate_features.R
Generates matrices summarizing connections between adducts and isotopes.
1 2 3 4 5 6  generate_connectivity_matrix(
info.features,
type,
ids.use = NULL,
ratios = FALSE
)

info.features 
data.frame with information about theoretical possible
features (e.g. as generated by the function

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). 
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.
1 2 3 4 5 6 7  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")

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