queryDGIdb: Query DGIdb using R

In rDGIdb: R Wrapper for DGIdb

Description

Provides an interface to query DGIdb from within R using the DGIdb API. The function is implemented to reflect the as good as possible the web-interface.

Usage

queryDGIdb(genes,
        sourceDatabases = NULL,
        geneCategories = NULL,
        interactionTypes = NULL)

Arguments

genes	A character vector of genes for which drug interactions are queried.
sourceDatabases	A character vector of source databases to be queried. To query all available databases, skip argument or use NULL. To see available options, type sourceDatabases().
geneCategories	A character vector of gene categories to be queried. To query for all gene categories, skip argument or use NULL. To see available options, type geneCategories().
interactionTypes	A character vector of interaction types to be queried. To query for all interaction types, skip argument or use NULL. To see available options, type interactionTypes().

Details

Only the first argument (genes) is required, all other arguments are optional. When optional arguments are not provided, the query considers all available possibilities for optional arguments: sourceDatabases, geneCategories, and interactionTypes.

Value

A S4 object of type rDGIdbResult.

Author(s)

Thomas Thurnherr <[e-mail]>

References

Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL, Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR, Wilson RK, Mardis ER, Griffith M, Griffith OL. DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Research. 2016 Jan 4;44(D1):D1036-44. doi:10.1093/nar/gkv1165.

See Also

rDGIdbResult, rDGIdbFilters, plotInteractionsBySource

Examples

genes <- c("XYZA", "TNF", "IL6", "IL8")
result <- queryDGIdb(genes = genes)

result <- queryDGIdb(genes = genes,
                sourceDatabases = c("MyCancerGenome","TEND","TTD"),
                geneCategories = "CELL SURFACE",
                interactionTypes = c("activator","inhibitor"))

rDGIdb documentation built on Nov. 8, 2020, 6:47 p.m.