inst/doc/brendaDb.R

In brendaDb: The BRENDA Enzyme Database

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)

## ---- eval=FALSE--------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("brendaDb", dependencies=TRUE)

## ---- setup, message=FALSE----------------------------------------------------
if(!requireNamespace("brendaDb")) {
  devtools::install_github("y1zhou/brendaDb")
}

## -----------------------------------------------------------------------------
library(brendaDb)

## ---- eval=FALSE--------------------------------------------------------------
#  brenda.filepath <- DownloadBrenda()
#  #> Please read the license agreement in the link below.
#  #>
#  #> https://www.brenda-enzymes.org/download_brenda_without_registration.php
#  #>
#  #> Found zip file in cache.
#  #> Extracting zip file...

## ---- eval=FALSE--------------------------------------------------------------
#  df <- ReadBrenda(brenda.filepath)
#  #> Reading BRENDA text file...
#  #> Converting text into a list. This might take a while...
#  #> Converting list to tibble and removing duplicated entries...
#  #> If you're going to use this data again, consider saving this table using data.table::fwrite().

## -----------------------------------------------------------------------------
brenda_txt <- system.file("extdata", "brenda_download_test.txt",
                          package = "brendaDb")
df <- ReadBrenda(brenda_txt)
res <- QueryBrenda(df, EC = c("1.1.1.1", "6.3.5.8"), n.core = 2)

res

res[["1.1.1.1"]]

## -----------------------------------------------------------------------------
ShowFields(df)

res <- QueryBrenda(df, EC = "1.1.1.1", fields = c("PROTEIN", "SUBSTRATE_PRODUCT"))
res[["1.1.1.1"]][["interactions"]][["substrate.product"]]

## -----------------------------------------------------------------------------
res <- QueryBrenda(df, EC = "1.1.1.1", organisms = "Homo sapiens")
res$`1.1.1.1`

## -----------------------------------------------------------------------------
res <- QueryBrenda(df, EC = c("1.1.1.1", "6.3.5.8"), n.core = 2)
ExtractField(res, field = "parameters$ph.optimum")

## -----------------------------------------------------------------------------
ID2Enzyme(brenda = df, ids = c("ADH4", "CD38", "pyruvate dehydrogenase"))

## -----------------------------------------------------------------------------
BiocycPathwayEnzymes(org.id = "HUMAN", pathway = "PWY66-400")

## -----------------------------------------------------------------------------
BiocycPathwayGenes(org.id = "HUMAN", pathway = "TRYPTOPHAN-DEGRADATION-1")

## ---- eval=FALSE--------------------------------------------------------------
#  EC.numbers <- head(unique(df$ID), 100)
#  system.time(QueryBrenda(df, EC = EC.numbers, n.core = 0))  # default
#  #  user  system elapsed
#  # 4.528   7.856  34.567
#  system.time(QueryBrenda(df, EC = EC.numbers, n.core = 1))
#  #  user  system elapsed
#  # 22.080   0.360  22.438
#  system.time(QueryBrenda(df, EC = EC.numbers, n.core = 2))
#  #  user  system elapsed
#  # 0.552   0.400  13.597
#  system.time(QueryBrenda(df, EC = EC.numbers, n.core = 4))
#  #  user  system elapsed
#  # 0.688   0.832   9.517
#  system.time(QueryBrenda(df, EC = EC.numbers, n.core = 8))
#  #  user  system elapsed
#  # 1.112   1.476  10.000

## -----------------------------------------------------------------------------
sessionInfo()