summarizeResponse: Summarize Response of PDXs

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

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,
  other.col = NULL,
  return.type = c("matrix", "data.frame")
)

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
other.col	Names of other columns to add in the return, if return.type is data.frame
return.type	Specify return type, allowed values are 'matrix' or 'data.frame'. Default 'matrix'

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")

## to get batch level response
br <- summarizeResponse(brca, response.measure = "abc", return.type="data.frame")

## to get model level response for a batch
r <- summarizeResponse(brca, response.measure = "mRECIST", batch.id = "X-1004.BGJ398")

bhklab/Xeva documentation built on Nov. 12, 2022, 5:38 a.m.