R: Summarize Response of PDXs

summarizeResponse {Xeva}

R Documentation

Summarize Response of PDXs

Description

This function summarizes the drug response information of PDXs.

Usage

summarizeResponse(object, response.measure = "mRECIST",
  model.id = NULL, batch.id = NULL, group.by = "patient.id",
  summary.stat = c(";", "mean", "median"), tissue = NULL)

Arguments

`object`	The `XevaSet` object.
`response.measure`	`character` indicating which response measure to use. Use the `responseMeasures` function to find out what measures are available for each `XevaSet`.
`model.id`	The `model.id` for which data is required.
`batch.id`	A `vector` of batch names. Default `NULL` will return all batches.
`group.by`	Default `patient.id`. Dictates how the models should be grouped together. See details below.
`summary.stat`	Dictates which summary method to use if multiple IDs are found.
`tissue`	Name of the tissue. Default `NULL`

Details

There can be two types of drug response measure.

Per model response: One response value for each Model, eg. mRECIST_recomputed for each model.
Per batch response: One response value for each Batch, eg. angle between treatment and control groups.

For the per model response output, columns will be model.id (or group.by). For the per batch response output, the group.by value can be "batch.name".

Value

A matrix with rows as drug names, column as group.by. Each cell contains response.measure for the pair.

Examples

data(brca)
brca.mR <- summarizeResponse(brca, response.measure = "mRECIST", group.by="patient.id")

[Package Xeva version 1.3.0 Index]