In tgirke/longevityDrugs: Drug Candidates Relevant for Longevity Genomics Project

BiocStyle::markdown()
options(width=100, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))

suppressPackageStartupMessages({
    library(longevityTools) 
    library(ggplot2) }) 

Introduction

This vignette is part of the NIA funded Longevity Genomics project. For more information on this project please visit its website here. The GitHub repository of the corresponding R package is available here and the most recent version of this vignette can be found here.

The data package longevityDrugs contains molecular structures and annotation information of longevity-associated drugs (LADs). An iterative process will be used to assemble, update and curate this data set long-term [@Backman2011-uw; @Cao2008-zo]. Most small molecules will be identified by integrating several large-scale community data sources such as data from drug databases (e.g. Drugbank), bioassay databases (e.g. PubChem Bioassay, ChEMBL), literature, drug-related gene expression fingerprints (e.g. LINCS), genetic (e.g. GWAS) and phenotype resources. This will also include nearest neighbors of LADs sharing with them structural, physicochemical or biological properties.

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Getting Started

Installation

The R software for running longevityDrugs and longevityTools can be downloaded from CRAN. The longevityTools package can be installed from the R console using the following biocLite install command.

source("http://bioconductor.org/biocLite.R") # Sources the biocLite.R installation script 
biocLite("tgirke/longevityTools", build_vignettes=FALSE, dependencies=FALSE) # Installs package from GitHub
biocLite("tgirke/longevityDrugs", build_vignettes=FALSE, dependencies=FALSE)

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Loading of required packages

library(RSQLite); library(ChemmineR); library(longevityDrugs)

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Load database

mypath <- system.file("extdata", "cmap.db", package="longevityDrugs")
conn <- initDb(mypath)

Query database

Retrieve compound structures

results <- getAllCompoundIds(conn)
sdfset <- getCompounds(conn, results, keepOrder=TRUE)
sdfset
plot(sdfset[1:4], print=FALSE)
as.data.frame(datablock2ma(datablock(sdfset)))[1:4,]

Retrieve compound properties

myfeat <- listFeatures(conn)
feat <- getCompoundFeatures(conn, results, myfeat)
feat[1:4,]

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Funding

This project is funded by NIH grant U24AG051129 awarded by the National Intitute on Aging (NIA).

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Version information

sessionInfo()

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References

tgirke/longevityDrugs documentation built on May 31, 2019, 9:07 a.m.