Add chemical distance matrices to the mmo object

This function reads cosine, DREAMS, and MS2DeepScore molecular networking outputs from MZmine, then transform the similarity to distance and adds the dissimilarity matrices to the mmo object.

Usage

AddChemDist(mmo, cos_dir = NULL, dreams_dir = NULL, m2ds_dir = NULL)

Arguments

mmo

The mmo object

cos_dir

Path to the cosine similarity CSV file from MZMine (molecular networking)

dreams_dir

Path to the DREAMS similarity CSV file from MZMine (molecular networking)

m2ds_dir

Path to the MS2DeepScore similarity CSV file from MZMine (molecular networking)

Value

The mmo object with dissimilarity matrices added (mmo$cos.dissim, mmo$dreams.dissim, mmo$m2ds.dissim)

Examples

if (FALSE) {
mmo <- AddChemDist(mmo, 
 cos_dir = "path/to/cosine_similarity.csv", 
 dreams_dir = "path/to/dreams_similarity.csv", 
 m2ds_dir = "path/to/ms2deepscore_similarity.csv"
)
}