Prepare features edges

Description

This function prepares molecular network edges by combining MS1-based and spectral similarity edges, adding entropy information, and standardizing column names. Edges represent relationships between features in the molecular network.

Usage

prepare_features_edges(
  input = get_params(step = "prepare_features_edges")\$files\$networks\$spectral\$edges\$raw,
  output = get_params(step =
    "prepare_features_edges")\$files\$networks\$spectral\$edges\$prepared,
  name_source = get_params(step = "prepare_features_edges")\$names\$source,
  name_target = get_params(step = "prepare_features_edges")\$names\$target
)

Arguments

input	Named list containing paths to edge files. Must have "ms1" and "spectral" elements pointing to respective edge files.
output	Character string path where prepared edges should be saved
name_source	Character string name of the source feature column in input files
name_target	Character string name of the target feature column in input files

Value

Character string path to the prepared edges file

Examples

library("tima")

copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
dir <- paste0(github, repo)
input_1 <- get_params(step = "prepare_features_edges")$files$networks$spectral$edges$raw$ms1
input_2 <- get_params(step = "prepare_features_edges")$files$networks$spectral$edges$raw$spectral
get_file(url = paste0(dir, input_1), export = input_1)
get_file(url = paste0(dir, input_2), export = input_2)
prepare_features_edges(
  input = list("ms1" = input_1, "spectral" = input_2)
)
unlink("data", recursive = TRUE)