buildCMAPdb: Build CMAP Database

In yduan004/customCMPdb: Customize and Query Compound Annotation Database

Description

This function builds a SQLite database named as 'cmap.db' that contains id mappings of cmap names to PubChem/DrugBank IDs as well as compound structure information.

Usage

buildCMAPdb(dest_dir = ".")

Arguments

dest_dir

character(1), destination directory under which the result SQLite database named as 'cmap.db' stored. The default is user's current working directory.

Details

For about 2/3 of the CMAP drugs, one can obtain their PubChem/DrugBank IDs from the DMAP site here: http://bio.informatics.iupui.edu/cmaps. Since this website is no longer supported, the processed CMAP name to PubChem and DrugBank ID mapping table is stored under the "inst/extdata" folder of this package named as "dmap_unique.txt". The SMILES strings for CMAP entries were obtained from ChemBank. Compounds were matched by names using the 'stringdist' library where cmap_name from CMAP were mapped to the closest name in ChemBank.

Value

write "cmap.db" SQLite database to the destination directory defined by user.

Examples

library(ChemmineR)
## Query database
# buildCMAPdb(dest_dir="./inst/scripts")
# conn <- initDb("/inst/scripts/cmap.db")
# 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,]

yduan004/customCMPdb documentation built on Feb. 3, 2022, 2:10 p.m.