bioassay-class: Class '"bioassay"'

In girke-lab/bioassayR: Cross-target analysis of small molecule bioactivity

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

girke-lab/bioassayR documentation built on Oct. 22, 2024, 8:13 a.m.