clue {slinky} | R Documentation |
Wrapper for clue.io REST calls
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)
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 |
cl |
Optional cluster object to parallelize this
operation. If verbose is TRUE, use this pattern in order for
progress bar to update:
|
verbose |
Do you want to know how things are going? Default is false. |
Data returned by Slinky.api as a data.frame
# 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))