createXevaSet {Xeva} | R Documentation

## XevaSet constructor

### Description

A constructor to create XevaSet. Only objects returned by this constructor are expected to work with the XevaSet methods.

### Usage

    createXevaSet(name, model = data.frame(), drug = data.frame(),
      experiment = data.frame(), expDesign = list(),
      modelSensitivity = data.frame(), batchSensitivity = data.frame(),
      molecularProfiles = list(), modToBiobaseMap = data.frame())

### Arguments

`name` | A `character` string detailing the name of the dataset.
`model` | A `data.frame` containing the annotations for all the models used in the experiment.
`drug` | A `data.frame` containing the annotations for all the drugs profiled in the dataset, across all data types.
`experiment` | A `data.frame` containing all experiment information.
`expDesign` | A list containing name of the batch, control and treatment model.id
`modelSensitivity` | A `data.frame` containing sensitivity for each model
`batchSensitivity` | A `data.frame` containing sensitivity for each batch
`molecularProfiles` | A `list` of `ExpressionSet` objects containing different molecular profiles.
`modToBiobaseMap` | A `data.frame` containing model.id corresponding Biobase object id and name of the molecularProfiles

### Details

This function creates a XevaSet object. It takes different model infromation and genomic data as input. For detailed discription of all varaibles please see Xeva vignette section "Creating new Xeva object"

### Value

Returns Xeva object

### Examples

    ## read raw data files containg PDX experiment information and genomic data
    model = read.csv(system.file("extdata", "model.csv", package = "Xeva"))
    drug = read.csv(system.file("extdata", "drug.csv", package = "Xeva"))
    experiment= read.csv(system.file("extdata", "experiments.csv", package = "Xeva"))
    expDesign=readRDS(system.file("extdata", "batch_list.rds", package = "Xeva"))
    RNASeq=readRDS(system.file("extdata", "rnaseq.rds", package = "Xeva"))
    modToBiobaseMap=read.csv(system.file("extdata", "modelToExpressionMap.csv", package = "Xeva"))

    ## create Xeva object
    xeva.set = createXevaSet(name="example xevaSet", model=model, drug=drug,
                             experiment=experiment, expDesign=expDesign,
                             molecularProfiles=list(RNASeq = RNASeq),
                             modToBiobaseMap = modToBiobaseMap)
    print(xeva.set)

[Package Xeva version 1.8.0 Index]