R: Summarize molecular profiles

summarizeMolecularProfiles {Xeva}

R Documentation

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)

[Package Xeva version 1.3.0 Index]