clue: clue

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

Description

Wrapper for clue.io REST calls

Usage

clue(x, endpoint = c("sigs", "cells", "genes", "perts", "plates",
  "profiles", "rep_drugs", "rep_drug_indications", "pcls"), fields = "",
  where_clause = NULL, ids = NULL, limit = 0, count = FALSE,
  unpack_sigs = TRUE, poscon = c("omit", "keep"), cl = NULL,
  verbose = FALSE)

## S4 method for signature 'Slinky'
clue(x, endpoint = c("sigs", "cells", "genes",
  "perts", "plates", "profiles", "rep_drugs", "rep_drug_indications",
  "pcls"), fields = "", where_clause = NULL, ids = NULL, limit = 0,
  count = FALSE, unpack_sigs = TRUE, poscon = c("omit", "keep"),
  cl = NULL, verbose = FALSE)

Arguments

x	a Slinky Object
endpoint	The endpoint to query. Default is 'sigs'.
fields	Optional vector of fields to return.
where_clause	Optional where_clause clause. Must be named list (e.g. list(field='value')
ids	Optional vector of ids to fetch for sigs or profiles endpoints. Should not be used together with where_clause or count.
limit	Optional limit to number of instances (samples to return
count	Should we just return the count of intances satisfying the query rather than the data? Default is FALSE.
unpack_sigs	The sigs endpoint returns multiple distil_ids per row. Should we unpack these to one per row?
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'
cl	Optional cluster object to parallelize this operation. If verbose is TRUE, use this pattern in order for progress bar to update: cl <- parallel::makeCluster(4, outfile=\"\")
verbose	Do you want to know how things are going? Default is false.

Value

Data returned by Slinky.api as a data.frame

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))

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