clueInstances: clueInstances

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

Description

Convenience wrapper to query function to retrieve instance ids meeting specified criteria.

Usage

clueInstances(x, where_clause = NULL, verbose = FALSE,
  poscon = c("omit", "keep"))

## S4 method for signature 'Slinky'
clueInstances(x, where_clause = NULL,
  verbose = FALSE, poscon = c("omit", "keep"))

Arguments

x	a Slinky Object
where_clause	Filter terms, as a list of terms, e.g. list(pert_type='trt_cp', 'is_gold'=TRUE). Terms will be joined by AND logic.
verbose	Do you want to know how things are going? Default is false.
poscon	Instances of type trt_poscon are recoded as trt_cp in clue.io's sigs endpoint. This can lead to unexpected results downstream. To keep these instances, specify poscon='keep'

Value

Vector of ids matching criteria. This is a convenience wrapper to the signature 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_ids <- clueInstances(sl, where_clause = list("pert_iname" = "amoxicillin", 
                                    "cell_id" = "MCF7",
                                    "is_gold" = TRUE))

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