ToxicoSet-class: Class to contain Toxico-genomic Data

In bhklab/ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

Class to contain Toxico-genomic Data

Description

The ToxicoSet (tSet) class was development to contain and organise large ToxicGenomic datasets as well as provide useful tools for interacting with this data. Functions are included for exploring the relationship between survival fraction and gene expression in cultured human and rat tissues during exposure to a wide ranges of compounds. Features include plotting dose and exposure time curves, calculating AUC, fitting linear models and computing sensitivity signatures.

Value

An object of the ToxicoSet class

Slots

annotation

A list of annotation data about the ToxicoSet, including the $name and the session information for how the object was creating, detailing the exact versions of R and all the packages used

molecularProfiles

A list containing SummarizedExperiment type object for holding data for RNA, DNA, SNP and CNV measurements, with associated fData and pData containing the row and column metadata

sample

A data.frame containing the annotations for all the cell lines profiled in the data set, across all data types

treatment

A data.frame containg the annotations for all the drugs profiled in the data set, across all data types

treatmentResponse

A list containing all the data for the sensitivity experiments, including $info, a data.frame containing the experimental info,$raw a 3D array containing raw data, $profiles, a data.frame containing sensitivity profiles statistics, and $n, a data.frame detailing the number of experiments for each cell-drug pair

perturbation

A list containting $n, a data.frame summarizing the available perturbation data,

curation

A list containing mappings for $treatment, sample, tissue names used in the data set to universal identifiers used between different ToxicoSet objects

datasetType

A character string of 'sensitivity', 'perturbation', or both detailing what type of data can be found in the ToxicoSet, for proper processing of the data

bhklab/ToxicoGx documentation built on March 18, 2023, 6:44 a.m.