RadioSet-class: A Class to Contain RadioGenomic datasets together with their...

In bhklab/RadioGx: Analysis of Large-Scale Radio-Genomic Data

A Class to Contain RadioGenomic datasets together with their curations

Description

The RadioSet (RSet) class was developed to contain and organise large RadioGenomic datasets, and aid in their metanalysis. It was designed primarily to allow bioinformaticians and biologists to work with data at the level of genes and cell lines, providing a more naturally intuitive interface and simplifying analyses between several datasets. As such, it was designed to be flexible enough to hold datasets of two different natures while providing a common interface. The class can accomidate datasets containing both radiation dose response data, as well as datasets contaning genetic profiles of cell lines pre and post treatement with compounds, known respecitively as sensitivity and perturbation datasets.

Value

An object of the RadioSet class

Slots

annotation

A list of annotation data about the RadioSet, 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 4 SummarizedExperiment type object for holding data for RNA, DNA, SNP and Copy Number Variation measurements respectively, with associated fData and pData containing the row and column metadata

sample

A data.frame containg 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 radiation treatment types used in the in the dataset, across all data types

sensitivity

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-radiation type pair

perturbation

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

curation

A list containing mappings for cell and tissue names used in the data set to universal identifiers used between different RadioSet objects

datasetType

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

bhklab/RadioGx documentation built on Oct. 6, 2023, 8:27 a.m.