Slinky-class {slinky} | R Documentation |
The Slinky
class encapsulates details about location of the LINCS L1000
data files as well as access credentials for the clue.io API (if desired).
It provides methods for querying and loading data from these resources.
The helper function Slinky
is a simpler way to construct
an object of this class
The Slinky()
constructor returns a slinky object with defaults
set where required. To access the clue.io API, you must either provide
your key as the value for the arguemtn user_key
, or set the
CLUE_API_KEY environment variable prior to starting your R session.
If no clue.io API access is required, simply specify user_key = ""
.
If info
is not specified, it will be assumed that the file
GSE92742_Broad_LINCS_inst_info.txt.gz is present in the working directory.
Slinky(user_key = character(), gctx = character(), info = character())
user_key |
clue.io API key |
gctx |
gctx containing expression data (optional) |
info |
info file containing metadata (optional) |
A Slinky object.
.index
internal slot for mapping object to file data
base
Base url for clue.io API.
gctx
gctx containing expression data (optional)
info
info file containing metadata (optional)
metadata
internal slot for storing metadata from info file, mapped to gctx file and current index.
user_key
clue.io API key (required unless CLUE_API_KEY env variable is set)
# 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_gold <- clueInstances(sl, where_clause = list('pert_type' = 'trt_cp', 'pert_iname' = 'amoxicillin', 'cell_id' = 'MCF7', 'is_gold' = TRUE), poscon = 'omit') amox_gold_sumexp <- loadL1K(sl, ids = amox_gold)