bioassay-class {bioassayR} | R Documentation

## Class `"bioassay"`

### Description

This class represents the data from a bioassay experiment, where a number of small molecules are screened against a defined target (such as a protein or living organism).

### Objects from the Class

Objects can be created by calls of the form `new("bioassay", ...)`.

### Slots

`aid`:

  Object of class `"character"` containing the assay id. For assays sourced from NCBI PubChem, this should be a string containing the PubChem AID (assay identifier).

`source_id`:

  Object of class `"character"`. This should match the description for a data source loaded via the `addDataSource()` function.

`assay_type`:

  Object of class `"character"`. A string noting the type of bioactivity experiment, such as “confirmatory” to represent a confirmatory assay.

`organism`:

  Object of class `"character"`. A string noting the scientific name of the assays target organism.

`scoring`:

  Object of class `"character"`. A string noting the scoring method used for the bioactivity experiment. For example, IC50 or EC50.

`targets`:

  Object of class `"character"`. A string or vector of strings containing the target identifier indicating the assay target. In the case of protein targeted assays sourced from NCBI PubChem, this should be a genbank ID.

`target_types`:

  Object of class `"character"`. A string of text or vector of strings, representing (in the same order) the target types for each target. For example “protein” or “cell.”

`scores`:

  Object of class `"data.frame"` containing the bioactivity data to be loaded. This must be a 3 column data frame, with each row representing the bioactivity results of a single molecule. The first column represents the compound id (cid), which must be a unique value for each structurally distinct molecule. The second column is a binary value representing activity (1=active, 0=inactive, NA=inconclusive or untested) for the given assay. The last column represents a score, scored by the method specified with the `addBioassay()` function. Missing or non-applicable values in any column should be represented by a `NA` value.

### Methods

aid

  `signature(x = "bioassay")`: ...

aid<-

  `signature(x = "bioassay")`: ...

assay_type

  `signature(x = "bioassay")`: ...

assay_type<-

  `signature(x = "bioassay")`: ...

organism

  `signature(object = "bioassay")`: ...

organism<-

  `signature(object = "bioassay")`: ...

scores

  `signature(x = "bioassay")`: ...

scores<-

  `signature(x = "bioassay")`: ...

scoring

  `signature(x = "bioassay")`: ...

scoring<-

  `signature(x = "bioassay")`: ...

show

  `signature(object = "bioassay")`: ...

source_id

  `signature(x = "bioassay")`: ...

source_id<-

  `signature(x = "bioassay")`: ...

target_types

  `signature(x = "bioassay")`: ...

target_types<-

  `signature(x = "bioassay")`: ...

targets

  `signature(x = "bioassay")`: ...

targets<-

  `signature(x = "bioassay")`: ...

### Author(s)

Tyler Backman

### See Also

Related classes: bioassaySet, bioAssayDB.

### Examples

    showClass("bioassay")

    ## create a new bioassay object from sample data
    data(samplebioassay)
    myassay <- new("bioassay",aid="1000", source_id="test", targets="116516899",
        target_types="protein", scores=samplebioassay)
    myassay

[Package bioassayR version 1.32.1 Index]