processDrugage: Process Source DrugAge Dataset

In yduan004/customCMPdb: Customize and Query Compound Annotation Database

Description

This function processes the source DrugAge datasets by adding the ChEMBL, PubChem and DrugBank id mapping information to the source DrugAge table which only has compound names without id mapping information. Source file of DrugAge is linked here: http://genomics.senescence.info/drugs/dataset.zip

Usage

processDrugage(dest_file = "drugage_id_mapping.tsv", verbose = TRUE)

Arguments

dest_file	character(1), file path to the generated DrugAge annotation tabular file with id mappings. The default will write the file named as "drugage_id_mapping.tsv" to user's current working directory.
verbose	logical(1), If descriptive message and list of issues should be included as output

Details

This function only annotates compound names that have ChEMBL ids from the ChEMBL database (version 24). The missing IDs were added manually. A semi-manual approach was to use this web service: https://cts.fiehnlab.ucdavis.edu/batch. After the semi-manual process, the left ones were manually mapped to ChEMBL, PubChem and DrugBank ids. The mixed items were commented.

Value

write the default 'drugage_id_mapping.tsv' file to user's current working directory or the file path defined by users to the dest_dafile argument.

Examples

library(ChemmineR)
## Not run: 
processDrugage(dest_file="drugage_id_mapping.tsv")
# Now the missing IDs need to be added manually. A semi-manual approach is to 
# use this web service: https://cts.fiehnlab.ucdavis.edu/batch

## End(Not run)

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