summarizeData: Summarize molecular profiles and drug response data

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

Summarize molecular profiles and drug response data

Description

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

Usage

summarizeData(
  object,
  drug,
  mDataType,
  tissue = NULL,
  sensitivity.measure = "all",
  sen.type = c("batch", "model"),
  unique.model = TRUE,
  batch = NULL,
  summarizedExp = FALSE
)

summarizeMolecularProfiles(...)

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 'all' will return all sensitivity measures.
sen.type	Type of sensitivity measure. Options are 'batch' (default) or 'model'
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.
summarizedExp	If TRUE will return SummarizedExperiment class object. Default TRUE will return ExpressionSet.

Details

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

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

Value

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

Examples

data(brca)

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

#to get all batch level response
pacRNA <- summarizeData(brca, drug="paclitaxel", mDataType="RNASeq",
                    tissue= "BRCA", sensitivity.measure="all")
print(pacRNA)

#to get all model level response
pacRNA <- summarizeData(brca, drug="paclitaxel", mDataType="RNASeq",
                    tissue= "BRCA", sensitivity.measure="all",
                    sen.type="model")
print(pacRNA)

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