data_raw/configure.R

In faustovrz/pglipid: Highland maize phosphoglycerolipid analysis

library(dplyr)
config_file <- file.path("..", "inst","config.yaml")
config_R    <- file.path("..", "R", "config.R")
read_col_R  <- file.path("..", "R", "read_col.R")
read_dat_R  <- file.path("..", "R", "read_dat.R")
gene_name_R <- file.path("..", "R", "gene_name.R")
genome_R    <- file.path("..", "R", "genome.R")
make_data_R <- file.path("..", "R", "make_data.R")

source(config_R)
source(read_col_R)
source(read_dat_R)
source(gene_name_R)
source(genome_R)

config <- get_config(config_file = config_file)

source(make_data_R)

pathways_col    <- make_pathways_col(config)
genes_col       <- make_genes_col(config)
enzymes_col     <- make_enzymes_col(config)
xref            <- make_xref(config)
corncyc_pathway <- make_corncyc_pathway(genes_col, pathways_col)
gene_synonym    <- make_corncyc_gene_synonym(genes_col)
enz_rxn_path    <- make_enz_rxn_path(enzymes_col)
proteins_dat    <- make_proteins_dat(config)
enz_rxn         <- make_enz_rxn(proteins_dat)
orphan_enz      <- make_orphan_enz( enz_rxn, enz_rxn_path)
map_id          <- make_map_id(config = config)


usethis::use_data(
  config,
  pathways_col,
  genes_col,
  xref,
  corncyc_pathway,
  gene_synonym,
  enz_rxn_path,
  enz_rxn,
  orphan_enz,
  map_id,
  internal =  TRUE,
  overwrite = TRUE
)