In patzaw/BED: Biological Entity Dictionary (BED)

library(knitr)
library(here)
library(BED)
library(dplyr)
cranRef <- function(x){
  sprintf(
    "[%s](https://CRAN.R-project.org/package=%s): %s",
    x, x, packageDescription(x)$Title
  )
}

Biological Entity Dictionary

r packageDescription("BED")$Description

Installation

From CRAN

install.packages("BED")

Dependencies

The following R packages available on CRAN are required:

deps <- desc::desc_get_deps()
sdeps <- filter(deps, type %in% c("Depends", "Imports") & package!="R")
for(p in sdeps$package){
   cat(paste("-", cranRef(p)), sep="\n")
}

And those are suggested:

wdeps <- filter(deps, type=="Suggests" & package!="R")
for(p in wdeps$package){
   cat(paste("-", cranRef(p)), sep="\n")
}

Installation from github

devtools::install_github("patzaw/BED")

Possible issue when updating from releases <= 1.3.0

If you get an error like the following...

Error: package or namespace load failed for ‘BED’:
 .onLoad failed in loadNamespace() for 'BED', details:
  call: connections[[connection]][["cache"]]
  error: subscript out of bounds

... remove the BED folder located here:

file.exists(file.path(Sys.getenv("HOME"), "R", "BED"))

Documentation

Documentation is provided in the BED vignette.

A public instance of the BED Neo4j database is provided for convenience and can be reached as follows:

library(BED)
connectToBed("https://genodesy.org/BED/", remember=TRUE, useCache=TRUE)
findBeids()

Citing BED

This package and the underlying research has been published in this peer reviewed article:

" target="_blank"> r sub('[[]', '(', sub('[]]', ')', format(citation("BED"), style="textVersion")))

Available BED database instance

An instance of the BED database (UCB-Human) has been built using the script provided in the BED R package.

This instance is focused on Homo sapiens, Mus musculus, Rattus norvegicus, Sus scrofa and Danio rerio organisms. It has been built from the following resources:

• Ensembl
• NCBI
• Uniprot
• biomaRt
• GEOquery

config <- jsonlite::read_json(
  here("supp/Build/Genodesy-instance/deploy_config.json")
)
zr <- config$ZENODO_RECORD

The Neo4j graph database is available as a dump file shared in Zenodo.

The following shell commands can be adapted according to user needs and called to get a running Neo4j container with a BED database instance.

ec <- readLines(here("supp/Build/S21-Deploy-from-Zenodo.sh"))
torm <- grep("^### usage: ", ec, value=FALSE)
stopifnot(length(torm) == 1)
torm <- c(torm, torm+1)
clines <- grep("## Config ----", ec)
stopifnot(length(clines) == 1)
clines <- seq(
  clines,
  grep("#+@", ec)[which(grep("#+@", ec) > clines)][1],
  by = 1
)
torm <- c(torm, clines)
ec <- ec[-torm]
for(n in names(config)){
  ec <- gsub(paste0("[$][{]?", n, "[}]?"), config[[n]], ec)
}
ec <- gsub("___ROOT___", "~", ec)
##
cat('```sh', sep="\n")
cat(ec, sep="\n")
cat('```', sep="\n")

Build a BED database instance

Building and feeding a BED database instance is achieved using scripts available in the "supp/Build" folder.

Run a neo4j docker images

Using the S01-NewBED-Container.sh script.

Build and feed BED

Using the S02-Rebuild-BED.sh script which compile the Rebuild-BED.Rmd document.

Dump the graph DB content for sharing

Using the S03-Dump-BED.sh script

Docker notes

Sergio Espeso-Gil has reported stability issues with Docker images in Windows. It's mainly solved by checking the "Use the WSL2 based engine" options in docker settings. More information is provided here: https://docs.docker.com/docker-for-windows/wsl/

patzaw/BED documentation built on April 30, 2024, 5:31 a.m.