rzs {slinky} | R Documentation

## rzs

### Description

Convert each sample in `treat` to robust zscore.

### Usage

    rzs(x, treat, control = "auto", where_clause = list(), gold = TRUE,
      inferred = TRUE, byplate = TRUE, verbose = FALSE, ...)

    ## S4 method for signature 'Slinky'
    rzs(x, treat, control = "auto", where_clause = list(),
      gold = TRUE, inferred = TRUE, byplate = TRUE, verbose = FALSE, ...)

### Arguments

`x` | An object of class Slinky
`treat` | A SummarizedExperiment containing the treated samples, or the pert_iname of desired perturbagen. See details.
`control` | An SummarizedExperiment containing the control samples, or the pert_iname of desired controls. Default is 'auto'. See details.
`where_clause` | If treat is a pert_iname, further query terms may be specified here (e.g. `pert_type=\"trt_sh\"`).
`gold` | Restrict analysis to gold instances as defined by LINCS. Ignored if treat and control are SummarizedExperiments.
`inferred` | Should the inferred (non-landmark) genes be included in the analysis? Default is TRUE.
`byplate` | Do you want to split the scores by plate? This is usually wise, unless you have already subsetted `treat` and `control` samples in such a way that plate can safely be ignored, or if `treat` and `control` must come from different plates for some reason. Default is TRUE.
`verbose` | Do you want to know how things are going? Default is FALSE.
`...` | Additional arguments for `method`.

### Value

Matrix of zscore of same dimension as `treat` (or the expression matrix resulting from querying for `treat` if a pert_iname is specified). This function identifes same-plate controls for each treated sample, then converts each treated sample to robust z-score by subtracting the median control values and dividing by the (scaled) median absolute deviations.

### 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'))
    scores <- rzs(sl, "amoxicillin")
    head(scores)

[Package slinky version 1.0.2 Index]