Description Usage Arguments Value Examples
Wrapper for clue.io REST calls
1 2 3 4 5 6 7 8 9 10 11 12 | 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
1 2 3 4 5 6 7 8 9 10 11 12 | # 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))
|
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