createXevaSet: XevaSet constructor

In bhklab/Xeva: Analysis of patient-derived xenograft (PDX) data

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)

bhklab/Xeva documentation built on Nov. 30, 2024, 3:17 a.m.