Slinky-class {slinky} | R Documentation

## An S4 class for working with LINCS data

### Description

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.

### Usage

    Slinky(user_key = character(), gctx = character(), info = character())

### Arguments

`user_key` | clue.io API key
`gctx` | gctx containing expression data (optional)
`info` | info file containing metadata (optional)

### Value

A Slinky object.

### Slots

`.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)

### 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_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)

[Package slinky version 1.0.2 Index]