Package 'brendaDb'

brendaDb: the BRENDA enzyme database.

Description

brendaDb provides an R interface to download, clean and extract enzyme information from the BRENDA database.

Details

The main aims of brendaDb include:

• Read text file downloaded from BRENDA into an R tibble

• Retrieve information for specific enzymes

• Query enzymes using their synonyms, gene symbols, etc.

• Query enzyme information for specific BioCyc pathways

To learn more about brendaDb, please refer to the vignette. browseVignettes(package = "brendaDb")

Author(s)

Maintainer: Yi Zhou [email protected] (ORCID)

See Also

Useful links:

• https://github.com/y1zhou/brendaDb

• Report bugs at https://github.com/y1zhou/brendaDb/issues

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Download and unzip the BRENDA text file.

Description

By default, the function downloads a zipped BRENDA text file to a local cache directory, and extracts a brenda_download.txt file.

Usage

DownloadBrenda(force.download = FALSE)

Arguments

force.download

Boolean value. If TRUE, ignore the cache and force re-download of the BRENDA text file. Default is FALSE.

Value

A string of the path to the downloaded BRENDA text file.

Examples

## Not run: DownloadBrenda()

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Extract a specific field from a brenda.entries object.

Description

Retrieve one field from all the brenda.entry objects. A column of EC numbers will be added to distinguish different enzymes.

Usage

ExtractField(res, field, entries = NULL)

Arguments

res	A brenda.entries object from QueryBrenda().
field	A string indicating the field to extract. Nested fields should be separated by $, e.g. parameters$ph.optimum.
entries	A character vector with values of EC numbers. This should be a subset of names(res).

Value

A tibble with all columns from the tibble in the given field, and extra columns containing the EC numbers and organisms.

Examples

df <- ReadBrenda(system.file("extdata", "brenda_download_test.txt",
                          package = "brendaDb"))
res <- QueryBrenda(brenda = df, EC = c("1.1.1.1", "6.3.5.8"),
                   n.core = 2)
ExtractField(res, field = "molecular$stability$general.stability")
ExtractField(res, field = "structure$subunits")

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A helper function for converting names/synonyms to EC numbers.

Description

A helper function for converting names/synonyms to EC numbers.

Usage

ID2Enzyme(brenda, ids)

Arguments

brenda	A tibble generated from ReadBrenda().
ids	A character vector of IDs to be converted.

Details

The function goes through "RECOMMENDED_NAME", "SYSTEMATIC_NAME", and "SYNONYMS" in the BRENDA file, and uses regexes to look for the given IDs. Values in the three columns are kept if the regex had a hit, otherwise NA is filled. The function can take in IDs of multiple sources, e.g. c("ADH4", "CD38", "pyruvate dehydrogenase"). Note that using aliases instead of symbols could lead to false positives in the output table.

Value

A tibble with columns ID, EC, and at least one of (RECOMMENDED_NAME, SYSTEMATIC_NAME and SYNONYMS).

Examples

df <- ReadBrenda(system.file("extdata", "brenda_download_test.txt",
                          package = "brendaDb"))
ID2Enzyme(df, c("CD38", "ADH4", "pyruvate dehydrogenase"))

---

Show the number of regular and transferred/deleted brenda.entry objects in the brenda.entries list.

Description

Show the number of regular and transferred/deleted brenda.entry objects in the brenda.entries list.

Usage

## S3 method for class 'brenda.entries'
print(x, ..., verbose = FALSE)

Arguments

x	A brenda.entries list returned by QueryBrenda().
...	Other arguments passed to the generic function.
verbose	Boolean; if TRUE, print tree views of brenda.query objects.

Value

Nothing; print summary information to the terminal.

---

Show the non-empty fields in the query result.

Description

For details, see PrettyPrintBrendaEntry().

Usage

## S3 method for class 'brenda.entry'
print(x, full.output = FALSE, ...)

Arguments

x	A brenda.entry object (elements in the list returned by the function QueryBrenda()).
full.output	A boolean default to FALSE. If TRUE, include all entries even if they are empty (NA or 0 rows).
...	Other arguments passed to the generic function.

Value

Nothing; print object information to the terminal.

---

Query for multiple enzymes.

Description

Use a vector of EC numbers to retrieve information from the BRENDA tibble read in by ReadBrenda(). Invalid EC numbers will be removed and a message will be generated.

Usage

QueryBrenda(brenda, EC, n.core = 0, fields = FALSE, ...)

Arguments

brenda	A tibble containing information from BRENDA.
EC	A string of the EC number.
n.core	Integer specifying the number of cores to use. Default is 0, which would result in using all available cores.
fields	A character vector indicating fields to parse. Default is FALSE, which would be returning all fields.
...	Other parameters passed to QueryBrendaBase().

Value

A list of brenda.entry objects.

See Also

QueryBrendaBase() ConfigBPCores() SelectOrganism()

Examples

df <- ReadBrenda(system.file("extdata", "brenda_download_test.txt",
                          package = "brendaDb"))
res <- QueryBrenda(brenda = df, EC = c("1.1.1.1", "1.1.1.10", "6.3.5.8"),
                   n.core = 2, organisms = "Homo sapiens")

---

Read BRENDA text file into matrix.

Description

For each EC entry, split the annotations into three columns:

• ID: EC number, e.g. 1.1.1.1

• field: the content of the information, e.g. protein, localization

• description: everything else

Usage

ReadBrenda(filepath, clean = TRUE)

Arguments

filepath	A string indicating the path to the text file.
clean	Boolean; if TRUE, run CleanECNumber() after reading the file.

Value

A matrix containing information about the EC entries.

Examples

brenda_txt <- system.file("extdata", "brenda_download_test.txt",
                          package = "brendaDb")
df <- ReadBrenda(brenda_txt)

---

Read raw BRENDA text file.

Description

Read file into buffer, and load all non-empty lines. Comment lines (starting with *) are skipped. The text file should be downloaded from https://www.brenda-enzymes.org/download_brenda_without_registration.php

Usage

ReadBrendaFile(filepath)

Arguments

filepath

A string indicating the path to the text file.

Value

A vector with each element being a line in the file.

---

Convert vector of lines to matrix.

Description

For each EC entry, split the annotations into three columns:

• ID: EC number, e.g. 1.1.1.1

• field: the content of the information, e.g. protein, localization

• description: everything else

Usage

SeparateEntries(lines)

Arguments

lines

The output vector from read_brenda_file.

Value

A vector<vector> containing information about the EC entries. In R this is a list of 3 lists.

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Show all unique BRENDA fields and their corresponding acronyms.

Description

Show all unique BRENDA fields and their corresponding acronyms.

Usage

ShowFields(df)

Arguments

df	A data.frame with columns "field" and "description"

Value

A data.frame with columns "field" and "acronym".

Examples

df <- ReadBrenda(system.file("extdata", "brenda_download_test.txt",
                          package = "brendaDb"))
ShowFields(df)

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