tests/testthat/test_id_conversion.R
In michaelwitting/wormLipidPredictR: Lipid reaction prediction based on WormJam
## define the mapping table
library(metaboliteIDmapping)
library(AnnotationHub)
ah <- AnnotationHub()
datasets <- query(ah, "metaboliteIDmapping")
annotation_set <- ah[["AH91792"]]
## function translate_id_to_ChEBI
test_that("translate_id_to_ChEBI works", {
ids <- c("HMDB0004947", "HMDB0004949", "HMDB0011763", "HMDB0004974", "HMDB0011594")
id_type <- "HMDB"
## run the function
translations <- translate_id_to_ChEBI(ids = ids, id_type = "HMDB",
annotation_set = annotation_set)
expect_equal(translations[["HMDB0004947"]], "72956")
expect_equal(translations[["HMDB0004949"]], "72959")
expect_equal(translations[["HMDB0011763"]], "74100")
expect_equal(translations[["HMDB0004974"]], "62107")
expect_equal(translations[["HMDB0011594"]], "62109")
translations <- translate_id_to_ChEBI(ids = ids, id_type = "CAS",
annotation_set = annotation_set)
expect_equal(translations[["HMDB0004947"]], "character(0)")
expect_equal(translations[["HMDB0004949"]], "character(0)")
expect_equal(translations[["HMDB0011763"]], "character(0)")
expect_equal(translations[["HMDB0004974"]], "character(0)")
expect_equal(translations[["HMDB0011594"]], "character(0)")
expect_error(translate_id_to_ChEBI(ids = ids, id_type = "foo",
annotation_set = annotation_set), "should be one of ")
expect_error(translate_id_to_ChEBI(ids = ids, id_type = "HMDB",
annotation_set = NULL), "should be one of ")
expect_error(translate_id_to_ChEBI(ids = ids, id_type = NULL,
annotation_set = NULL), "applied to an object of class")
})
## function translate_ChEBI_to_SMILES
test_that("translate_ChEBI_to_SMILES works", {
ids <- list("HMDB0004947" = "72956", "HMDB0004949" = "72959",
"HMDB0011763" = "74100", "HMDB0004974" = "62107",
"HMDB0011594" = "62109")
## load rhea_chebi_smiles
file <- file.path(
path.package("LipidNetworkPredictR"), "extdata", "rhea-chebi-smiles.tsv",
fsep = .Platform$file.sep)
rhea_chebi_smiles <- read.csv(file, sep = "\t", header = FALSE)
## run the function
translations <- translate_ChEBI_to_SMILES(ids = ids, rhea_chebi_smiles = rhea_chebi_smiles)
expect_equal(translations[["HMDB0004947"]], "CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCC")
expect_equal(translations[["HMDB0004949"]], "CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCCCCCC")
expect_equal(translations[["HMDB0011763"]], "CCCCCCCC/C=C\\CCCCCCCC(=O)N[C@@H](CO)[C@H](O)CCCCCCCCCCCCCCC")
expect_equal(translations[["HMDB0004974"]], NA)
expect_equal(translations[["HMDB0011594"]], NA)
translations <- translate_ChEBI_to_SMILES(ids = ids, rhea_chebi_smiles = NULL)
expect_equal(translations[["HMDB0004947"]], NA)
expect_equal(translations[["HMDB0004949"]], NA)
expect_equal(translations[["HMDB0011763"]], NA)
expect_equal(translations[["HMDB0004974"]], NA)
expect_equal(translations[["HMDB0011594"]], NA)
expect_error(
translate_ChEBI_to_SMILES(ids = NULL, rhea_chebi_smiles = rhea_chebi_smiles),
"is not a list")
expect_equal(
translate_ChEBI_to_SMILES(ids = list(), rhea_chebi_smiles = rhea_chebi_smiles),
list())
})
## function select_substrates_or_products
test_that("select_substrates_or_products works", {
## given a rection that describes the change of (3S)-3-Hydroxy-2-butanone
## to its stereoisomer (3R)-3-Hydroxy-2-butanone
reaction <- list(c("CC(=O)[C@H](C)O", "CC(=O)[C@@H](C)O"))
## cols = 2
cols <- 2
res <- LipidNetworkPredictR:::select_substrates_or_products(reaction = reaction,
cols = cols, type = "substrates")
expect_equal(length(res), 1)
expect_equal(res[[1]], "CC(=O)[C@H](C)O")
res <- LipidNetworkPredictR:::select_substrates_or_products(reaction = reaction,
cols = cols, type = "products")
expect_equal(length(res), 1)
expect_equal(res[[1]], "CC(=O)[C@@H](C)O")
## cols = 3
cols <- 3
res <- LipidNetworkPredictR:::select_substrates_or_products(reaction = reaction,
cols = cols, type = "substrates")
expect_equal(length(res), 1)
expect_equal(res[[1]], "CC(=O)[C@@H](C)O")
res <- LipidNetworkPredictR:::select_substrates_or_products(reaction = reaction,
cols = cols, type = "products")
expect_equal(length(res), 1)
expect_equal(res[[1]], "CC(=O)[C@H](C)O")
})
## function find_RHEA_ids_from_SMILES
test_that("find_RHEA_ids_from_SMILES works", {
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$file.sep)
rhea_directions <- read.csv(file, sep = "\t", header = TRUE)
## run the function
## type = "both"
res <- find_RHEA_ids_from_SMILES(ids = ids,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "both")
expect_equal(res[["HMDB0004947"]],
c(41292, 41293, 70256, 70257, 70308, 70309))
expect_equal(res[["HMDB0004949"]],
c(38892, 38893, 45721, 45722, 46341, 46342, 36688, 36689, 45645, 45646,
58297, 58298, 58317, 58318, 69700, 69701, 69704, 69705))
expect_equal(res[["HMDB0011763"]],
c(45373, 45374, 36576, 36577))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
## type = "substrates"
res <- find_RHEA_ids_from_SMILES(ids = ids,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "substrates")
expect_equal(res[["HMDB0004947"]],
c(41292, 41293))
expect_equal(res[["HMDB0004949"]],
c(38892, 38893, 45721, 45722, 46341, 46342))
expect_equal(res[["HMDB0011763"]],
c(45373, 45374))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
## type = "products"
res <- find_RHEA_ids_from_SMILES(ids = ids,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "products")
expect_equal(res[["HMDB0004947"]],
c(70256, 70257, 70308, 70309))
expect_equal(res[["HMDB0004949"]],
c(36688, 36689, 45645, 45646, 45721, 45722, 58297, 58298, 58317, 58318,
69700, 69701, 69704, 69705))
expect_equal(res[["HMDB0011763"]],
c(36576, 36577))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
})
## function find_RHEA_ids_from_ids
test_that("find_RHEA_ids_from_ids works", {
ids <- c("HMDB0004947", "HMDB0004949", "HMDB0011763", "HMDB0004974", "HMDB0011594")
id_type <- "HMDB"
## load rhea_chebi_smiles
file <- file.path(
path.package("LipidNetworkPredictR"), "extdata", "rhea-chebi-smiles.tsv",
fsep = .Platform$file.sep)
rhea_chebi_smiles <- read.csv(file, sep = "\t", header = FALSE)
## 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"
res <- find_RHEA_ids_from_ids(ids = ids, id_type = id_type,
annotation_set = annotation_set, rhea_chebi_smiles = rhea_chebi_smiles,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "both")
expect_equal(res[["HMDB0004947"]],
c(41292, 41293, 70256, 70257, 70308, 70309))
expect_equal(res[["HMDB0004949"]],
c(38892, 38893, 45721, 45722, 46341, 46342, 36688, 36689, 45645, 45646,
58297, 58298, 58317, 58318, 69700, 69701, 69704, 69705))
expect_equal(res[["HMDB0011763"]],
c(45373, 45374, 36576, 36577))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
## type = "substrates"
res <- find_RHEA_ids_from_ids(ids = ids, id_type = id_type,
annotation_set = annotation_set, rhea_chebi_smiles = rhea_chebi_smiles,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "substrates")
expect_equal(res[["HMDB0004947"]],
c(41292, 41293))
expect_equal(res[["HMDB0004949"]],
c(38892, 38893, 45721, 45722, 46341, 46342))
expect_equal(res[["HMDB0011763"]],
c(45373, 45374))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
## type = "products"
res <- find_RHEA_ids_from_ids(ids = ids, id_type = id_type,
annotation_set = annotation_set, rhea_chebi_smiles = rhea_chebi_smiles,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "products")
expect_equal(res[["HMDB0004947"]],
c(70256, 70257, 70308, 70309))
expect_equal(res[["HMDB0004949"]],
c(36688, 36689, 45645, 45646, 45721, 45722, 58297, 58298, 58317, 58318,
69700, 69701, 69704, 69705))
expect_equal(res[["HMDB0011763"]],
c(36576, 36577))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
})
michaelwitting/wormLipidPredictR documentation built on Jan. 30, 2025, 12:30 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## define the mapping table
library(metaboliteIDmapping)
library(AnnotationHub)
ah <- AnnotationHub()
datasets <- query(ah, "metaboliteIDmapping")
annotation_set <- ah[["AH91792"]]
## function translate_id_to_ChEBI
test_that("translate_id_to_ChEBI works", {
ids <- c("HMDB0004947", "HMDB0004949", "HMDB0011763", "HMDB0004974", "HMDB0011594")
id_type <- "HMDB"
## run the function
translations <- translate_id_to_ChEBI(ids = ids, id_type = "HMDB",
annotation_set = annotation_set)
expect_equal(translations[["HMDB0004947"]], "72956")
expect_equal(translations[["HMDB0004949"]], "72959")
expect_equal(translations[["HMDB0011763"]], "74100")
expect_equal(translations[["HMDB0004974"]], "62107")
expect_equal(translations[["HMDB0011594"]], "62109")
translations <- translate_id_to_ChEBI(ids = ids, id_type = "CAS",
annotation_set = annotation_set)
expect_equal(translations[["HMDB0004947"]], "character(0)")
expect_equal(translations[["HMDB0004949"]], "character(0)")
expect_equal(translations[["HMDB0011763"]], "character(0)")
expect_equal(translations[["HMDB0004974"]], "character(0)")
expect_equal(translations[["HMDB0011594"]], "character(0)")
expect_error(translate_id_to_ChEBI(ids = ids, id_type = "foo",
annotation_set = annotation_set), "should be one of ")
expect_error(translate_id_to_ChEBI(ids = ids, id_type = "HMDB",
annotation_set = NULL), "should be one of ")
expect_error(translate_id_to_ChEBI(ids = ids, id_type = NULL,
annotation_set = NULL), "applied to an object of class")
})
## function translate_ChEBI_to_SMILES
test_that("translate_ChEBI_to_SMILES works", {
ids <- list("HMDB0004947" = "72956", "HMDB0004949" = "72959",
"HMDB0011763" = "74100", "HMDB0004974" = "62107",
"HMDB0011594" = "62109")
## load rhea_chebi_smiles
file <- file.path(
path.package("LipidNetworkPredictR"), "extdata", "rhea-chebi-smiles.tsv",
fsep = .Platform$file.sep)
rhea_chebi_smiles <- read.csv(file, sep = "\t", header = FALSE)
## run the function
translations <- translate_ChEBI_to_SMILES(ids = ids, rhea_chebi_smiles = rhea_chebi_smiles)
expect_equal(translations[["HMDB0004947"]], "CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCC")
expect_equal(translations[["HMDB0004949"]], "CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCCCCCC")
expect_equal(translations[["HMDB0011763"]], "CCCCCCCC/C=C\\CCCCCCCC(=O)N[C@@H](CO)[C@H](O)CCCCCCCCCCCCCCC")
expect_equal(translations[["HMDB0004974"]], NA)
expect_equal(translations[["HMDB0011594"]], NA)
translations <- translate_ChEBI_to_SMILES(ids = ids, rhea_chebi_smiles = NULL)
expect_equal(translations[["HMDB0004947"]], NA)
expect_equal(translations[["HMDB0004949"]], NA)
expect_equal(translations[["HMDB0011763"]], NA)
expect_equal(translations[["HMDB0004974"]], NA)
expect_equal(translations[["HMDB0011594"]], NA)
expect_error(
translate_ChEBI_to_SMILES(ids = NULL, rhea_chebi_smiles = rhea_chebi_smiles),
"is not a list")
expect_equal(
translate_ChEBI_to_SMILES(ids = list(), rhea_chebi_smiles = rhea_chebi_smiles),
list())
})
## function select_substrates_or_products
test_that("select_substrates_or_products works", {
## given a rection that describes the change of (3S)-3-Hydroxy-2-butanone
## to its stereoisomer (3R)-3-Hydroxy-2-butanone
reaction <- list(c("CC(=O)[C@H](C)O", "CC(=O)[C@@H](C)O"))
## cols = 2
cols <- 2
res <- LipidNetworkPredictR:::select_substrates_or_products(reaction = reaction,
cols = cols, type = "substrates")
expect_equal(length(res), 1)
expect_equal(res[[1]], "CC(=O)[C@H](C)O")
res <- LipidNetworkPredictR:::select_substrates_or_products(reaction = reaction,
cols = cols, type = "products")
expect_equal(length(res), 1)
expect_equal(res[[1]], "CC(=O)[C@@H](C)O")
## cols = 3
cols <- 3
res <- LipidNetworkPredictR:::select_substrates_or_products(reaction = reaction,
cols = cols, type = "substrates")
expect_equal(length(res), 1)
expect_equal(res[[1]], "CC(=O)[C@@H](C)O")
res <- LipidNetworkPredictR:::select_substrates_or_products(reaction = reaction,
cols = cols, type = "products")
expect_equal(length(res), 1)
expect_equal(res[[1]], "CC(=O)[C@H](C)O")
})
## function find_RHEA_ids_from_SMILES
test_that("find_RHEA_ids_from_SMILES works", {
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$file.sep)
rhea_directions <- read.csv(file, sep = "\t", header = TRUE)
## run the function
## type = "both"
res <- find_RHEA_ids_from_SMILES(ids = ids,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "both")
expect_equal(res[["HMDB0004947"]],
c(41292, 41293, 70256, 70257, 70308, 70309))
expect_equal(res[["HMDB0004949"]],
c(38892, 38893, 45721, 45722, 46341, 46342, 36688, 36689, 45645, 45646,
58297, 58298, 58317, 58318, 69700, 69701, 69704, 69705))
expect_equal(res[["HMDB0011763"]],
c(45373, 45374, 36576, 36577))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
## type = "substrates"
res <- find_RHEA_ids_from_SMILES(ids = ids,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "substrates")
expect_equal(res[["HMDB0004947"]],
c(41292, 41293))
expect_equal(res[["HMDB0004949"]],
c(38892, 38893, 45721, 45722, 46341, 46342))
expect_equal(res[["HMDB0011763"]],
c(45373, 45374))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
## type = "products"
res <- find_RHEA_ids_from_SMILES(ids = ids,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "products")
expect_equal(res[["HMDB0004947"]],
c(70256, 70257, 70308, 70309))
expect_equal(res[["HMDB0004949"]],
c(36688, 36689, 45645, 45646, 45721, 45722, 58297, 58298, 58317, 58318,
69700, 69701, 69704, 69705))
expect_equal(res[["HMDB0011763"]],
c(36576, 36577))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
})
## function find_RHEA_ids_from_ids
test_that("find_RHEA_ids_from_ids works", {
ids <- c("HMDB0004947", "HMDB0004949", "HMDB0011763", "HMDB0004974", "HMDB0011594")
id_type <- "HMDB"
## load rhea_chebi_smiles
file <- file.path(
path.package("LipidNetworkPredictR"), "extdata", "rhea-chebi-smiles.tsv",
fsep = .Platform$file.sep)
rhea_chebi_smiles <- read.csv(file, sep = "\t", header = FALSE)
## 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"
res <- find_RHEA_ids_from_ids(ids = ids, id_type = id_type,
annotation_set = annotation_set, rhea_chebi_smiles = rhea_chebi_smiles,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "both")
expect_equal(res[["HMDB0004947"]],
c(41292, 41293, 70256, 70257, 70308, 70309))
expect_equal(res[["HMDB0004949"]],
c(38892, 38893, 45721, 45722, 46341, 46342, 36688, 36689, 45645, 45646,
58297, 58298, 58317, 58318, 69700, 69701, 69704, 69705))
expect_equal(res[["HMDB0011763"]],
c(45373, 45374, 36576, 36577))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
## type = "substrates"
res <- find_RHEA_ids_from_ids(ids = ids, id_type = id_type,
annotation_set = annotation_set, rhea_chebi_smiles = rhea_chebi_smiles,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "substrates")
expect_equal(res[["HMDB0004947"]],
c(41292, 41293))
expect_equal(res[["HMDB0004949"]],
c(38892, 38893, 45721, 45722, 46341, 46342))
expect_equal(res[["HMDB0011763"]],
c(45373, 45374))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
## type = "products"
res <- find_RHEA_ids_from_ids(ids = ids, id_type = id_type,
annotation_set = annotation_set, rhea_chebi_smiles = rhea_chebi_smiles,
rhea_reaction_smiles = rhea_reaction_smiles,
rhea_directions = rhea_directions, type = "products")
expect_equal(res[["HMDB0004947"]],
c(70256, 70257, 70308, 70309))
expect_equal(res[["HMDB0004949"]],
c(36688, 36689, 45645, 45646, 45721, 45722, 58297, 58298, 58317, 58318,
69700, 69701, 69704, 69705))
expect_equal(res[["HMDB0011763"]],
c(36576, 36577))
expect_equal(res[["HMDB0004974"]], NA)
expect_equal(res[["HMDB0011594"]], NA)
})
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.