## ---- 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()