Create metabolite sets from existing genesets — make_gene_metab

Gene to metabolite translation is based on mappings in Recon-3D (cosmosR).

Usage

make_gene_metab_set(
  input_pk,
  metadata_info = c(Target = "gene"),
  pk_name = NULL,
  save_table = "csv",
  path = NULL
)

input_pk: dataframe with two columns for source (=term) and Target (=gene), e.g. Hallmarks.
metadata_info: Optional: Column name of Target in input_pk. Default = c(Target="gene")
pk_name: Optional: Name of the prior knowledge resource. default: NULL
save_table: Optional: File types for the analysis results are: "csv", "xlsx", "txt". Default = "csv"
path: Optional: String which is added to the resulting folder name default: NULL

List of two data frames: "GeneMetabSet" and "MetabSet".

data(hallmarks)
make_gene_metab_set(hallmarks)