Slinky-class: An S4 class for working with LINCS data
In erikor/slinky: Putting the fun in LINCS L1000 data analysis

Description Usage Arguments Value Slots Examples

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

1 2	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)