buildCMAPdb: Build structure database (e.g. CMAP)

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

Description

Function to build SQLite database containing small molecule structures, properties and annotations.

Usage

buildCMAPdb(rerun)

Arguments

rerun

Set rerun=TRUE to build database.

Details

...

Value

SQLite database

Author(s)

Thomas Girke

References

ChemmineR: https://www.bioconductor.org/packages/release/bioc/html/ChemmineR.html

Examples

## Build database
library(RSQLite); library(ChemmineR)
buildCMAPdb(rerun=FALSE) # Set to TRUE

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

## Query database
results <- getAllCompoundIds(conn)
sdfset <- getCompounds(conn, results, keepOrder=TRUE)
sdfset
as.data.frame(datablock2ma(datablock(sdfset)))[1:4,]
myfeat <- listFeatures(conn)
feat <- getCompoundFeatures(conn, results, myfeat)
feat[1:4,]

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