get_targets: Target Gene/Protein IDs for Query Drugs

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Target Gene/Protein IDs for Query Drugs

Description

This function returns for a set of query drug names/ids the corresponding target gene/protein ids. The required drug-target annotations are from DrugBank, CLUE and STITCH. An SQLite database storing these drug-target interactions based on the above three annotation resources is available in the signatureSearchData package.

Usage

get_targets(drugs, database = "all", verbose = TRUE, output = "df")

Arguments

drugs	character vector of drug names
database	drug-target annotation resource; A character vector of any combination of 'DrugBank', 'CLUE', STITCH' or 'all'. The target set from the selected resources will be combined. If 'all' is contained in the character vector, target sets from all of the annotation databases (DrugBank, CLUE and STITCH) will be combined.
verbose	TRUE or FALSE, whether to print messages
output	one of "df", "list" or "vector". If setting as "df", the result is in a data.frame format containing target gene symbols separated by semicolon for each drug. If setting as "list", the result is a list of targets for each query drug. If setting as "vector", the result is a character vector of the target set that are collapsed with duplications if different drugs have the same targets.

Value

drug-target annotation in a format defined by the output argument.

See Also

dtlink_db_clue_sti

Examples

data(drugs10)
dt <- get_targets(drugs10)

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.