controls {slinky} | R Documentation

## controls #' Fetch the same plate control samples applicable for given ids (distil_id). Expects that the specified ids have pert_type of trt_sh or trt_cp.

### Description

controls #' Fetch the same plate control samples applicable for given ids (distil_id). Expects that the specified ids have pert_type of trt_sh or trt_cp.

### Usage

    controls(x, ids, verbose = FALSE, cl = NULL)

    ## S4 method for signature 'Slinky'
    controls(x, ids, verbose = FALSE, cl = NULL)

### Arguments

`x` | A slinky object
`ids` | The distil_id(s) to lookup.
`verbose` | Do you want to know how things are going? Default is FALSE.
`cl` | Optional cluster object to parallelize this operation. If verbose is TRUE, use this pattern in order for progress bar to update: `cl <- parallel::makeCluster(4, outfile=\"\")`

### Value

The name of the vehicle control for the queried perturbagen(s). \For a given set of distil_ids, this function finds the distil_ids for the corresponding control samples based on the the pert_type and (for trt_cp) the specified vehicle. The returned dataframe can be used, among other things, to create a control dataset for differential expression or other analysis. See also diffexp.

### 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')$user_key
    sl <- Slinky(user_key,
                     system.file('extdata', 'demo.gctx',
                          package='slinky'),
                     system.file('extdata', 'demo_inst_info.txt',
                         package = 'slinky'))
    amox_gold <- clueInstances(sl, where_clause = list("pert_type" = "trt_cp",
       "pert_iname" = "amoxicillin",
       "cell_id" = "MCF7",
       "is_gold" = TRUE),
       poscon = "omit")
    colnames(sl[,1:5])
    rownames(sl[1:5,1:5])
    ids.ctrl <- controls(sl, ids = amox_gold)$distil_id

[Package slinky version 1.2.2 Index]