find_RHEA_ids_from_SMILES: Find RHEA ids from SMILES

In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam

Find RHEA ids from SMILES

Description

The function find_RHEA_ids_from_SMILES returns the RHEA ids that are involved in reactions of the given SMILES (ids).

Usage

find_RHEA_ids_from_SMILES(
  ids,
  rhea_reaction_smiles,
  rhea_directions,
  type = c("both", "substrates", "products")
)

Arguments

ids	list, entries contain the SMILES identifiers.
rhea_reaction_smiles	data.frame containing the mappings between ChEBI identifiers and SMILES identifiers
rhea_directions	data.frame containing information on the directionality of RHEA directions
type	character(1), one of "both", "substrates", or "products"

Details

The returned result might differ depending on the type object:

• if type = "both", the function will return the RHEA identifiers for the SMILES found both in the substrates or products of the reactions,

• if type = "substrates", the function will return the RHEA identifiers for the SMILES found in the substrates of the reactions,

• if type = "products", the function will return the RHEA identifiers for the SMILES found in the products of the reactions.

Value

list

Author(s)

Thomas Naake

Examples

ids <- list(
    "HMDB0004947" = "CCCCCCCCCCCCC/C=C/[C@H](O)[C@H](CO)NC(=O)CCCCCCCCCCC",
    "HMDB0004949" = "CCCCCCCCCCCCC/C=C/[C@H](O)[C@H](CO)NC(=O)CCCCCCCCCCCCCCC",
    "HMDB0011763" = "CCCCCCCC/C=C\\CCCCCCCC(=O)N[C@H](CO)[C@H](O)CCCCCCCCCCCCCCC",
    "HMDB0004974" = NA, 
    "HMDB0011594" = NA)
    
## rhea_reaction_smiles
file <- file.path(
    path.package("LipidNetworkPredictR"), "extdata", "rhea-reaction-smiles.tsv",
    fsep = .Platform$file.sep)
rhea_reaction_smiles <- read.csv(file, sep = "\t", header = FALSE)

## rhea_directions
file <- file.path(
    path.package("LipidNetworkPredictR"), "extdata", "rhea-directions.tsv",
    fsep = .Platform$file.sep)
rhea_directions <- read.csv(file, sep = "\t", header = TRUE)

## run the function
## type = "both"
find_RHEA_ids_from_SMILES(ids = ids, 
    rhea_reaction_smiles = rhea_reaction_smiles,
    rhea_directions = rhea_directions, type = "both")
## type = "substrates"
find_RHEA_ids_from_SMILES(ids = ids, 
    rhea_reaction_smiles = rhea_reaction_smiles,
    rhea_directions = rhea_directions, type = "substrates")
## type = "products"
find_RHEA_ids_from_SMILES(ids = ids, 
    rhea_reaction_smiles = rhea_reaction_smiles,
    rhea_directions = rhea_directions, type = "products")

michaelwitting/wormLipidPredictR documentation built on Aug. 28, 2024, 9:39 a.m.