clueVehicle: clueVehicle

In VanAndelInstitute/slinky: Putting the fun in LINCS L1000 data analysis

Description

Fetch the vehicle control applicable to given ids (distil_id). Expects that perturbagen is of type trt_cp.

Usage

clueVehicle(x, ids, verbose = FALSE)

## S4 method for signature 'Slinky'
clueVehicle(x, ids, verbose = FALSE)

Arguments

x	a Slinky Object
ids	The distil_id(s) to lookup.
verbose	Do you want to know how things are going? Default is FALSE.

Value

The name of the vehicle control for the queried perturbagen(s). This is a convenience wrapper to the profiles API which queries clue.io and unwraps response.

Examples

# for build/demo only.  You MUST use your own key when using the slinky
# package.
user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
                          as='parsed')$user_key
sl <- Slinky(user_key,
                 system.file('extdata', 'demo.gctx',
                      package='slinky'),
                 system.file('extdata', 'demo_inst_info.txt',
                     package = 'slinky'))
amox <- clue(sl, where_clause = list("pert_iname" = "amoxicillin", 
                                    "cell_id" = "MCF7",
                                    "is_gold" = TRUE))
amox.ctrl <- clueVehicle(sl, amox$distil_id)

VanAndelInstitute/slinky documentation built on Aug. 20, 2021, 1:05 p.m.