summarizeMolecularProfiles: Summarize molecular profiles

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

Summarize molecular profiles

Description

This function serves to get molecular profiles from a XevaSet object.

Usage

summarizeMolecularProfiles(
  object,
  drug,
  mDataType,
  tissue = NULL,
  sensitivity.measure = NULL,
  unique.model = TRUE,
  batch = NULL
)

Arguments

object	The XevaSet.
drug	Name of the drug.
mDataType	character, where one of the molecular data types is needed.
tissue	Default NULL will return all tissue types.
sensitivity.measure	Default NULL will return all sensitivity measures.
unique.model	Default TRUE will return only one sequncing ID, in the case where one model ID maps to several sequencing IDs.
batch	Name of the batch. Default NULL.

Details

• If a sequencing sample belongs to multiple models, summarizeMolecularProfiles will create a separate column for each model.

• All models without molecular data will be removed from the output ExpressionSet.

Value

An ExpressionSet where sample names are model.id and sensitivity measures will be presented in pData.

Examples

data(brca)
pacRNA <- summarizeMolecularProfiles(brca, drug="paclitaxel", mDataType="RNASeq",
                                     tissue= "BRCA", sensitivity.measure="mRECIST")
print(pacRNA)

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