get_targets: Target Gene/Protein IDs for Query Drugs

In signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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, collapse = FALSE)

Arguments

drugs	character vector of drug names
database	drug-target annotation resource; one of 'DrugBank', 'CLUE', 'STITCH' or 'all'. If 'all', the targets from DrugBank, CLUE and STITCH databases will be combined.
verbose	TRUE or FALSE, whether to print messages
collapse	TRUE or FALSE. If setting as FALSE, the result is a data.frame of target gene symbols of each drug. If TRUE, the targets are collapsed to be a character vector with duplications if different drugs have the same targets.

Value

data.frame, one column contains the query drug names and the other target gene symbols if collapse is FALSE. A character vetor if collapse is TRUE.

See Also

dtlink_db_clue_sti

Examples

data(drugs10)
dt <- get_targets(drugs10)

signatureSearch documentation built on April 16, 2021, 6 p.m.