summarizeSensitivityProfiles-RadioSet-method: Takes the sensitivity data from a RadioSet, and summarises...

In RadioGx: Analysis of Large-Scale Radio-Genomic Data

Description

This function creates a table with cell lines as rows and radiation types as columns, summarising the drug senstitivity data of a RadioSet into drug-cell line pairs

Usage

## S4 method for signature 'RadioSet'
summarizeSensitivityProfiles(
  object,
  sensitivity.measure = "AUC_recomputed",
  cell.lines,
  radiation.types,
  summary.stat = c("mean", "median", "first", "last", "max", "min"),
  fill.missing = TRUE,
  verbose = TRUE
)

Arguments

object	['RadioSet'] The RadioSet from which to extract the data
sensitivity.measure	['character'] which sensitivity sensitivity.measure to use? Use the sensitivityMeasures function to find out what measures are available for each PSet.
cell.lines	['character'] The cell lines to be summarized. If any cell lines has no data, it will be filled with missing values
radiation.types	['character'] The radiation types to be summarized. If any radiation type has no data, it will be filled with missing values
summary.stat	['character'] which summary method to use if there are repeated cell line-drug experiments? Choices are "mean", "median", "first", or "last"
fill.missing	['boolean'] should the missing cell lines not in the molecular data object be filled in with missing values?
verbose	Should the function print progress messages?

Value

[matrix] A matrix with cell lines going down the rows, radiation types across the columns, with the selected sensitivity statistic for each pair.

Examples

data(clevelandSmall)
GDSCauc <- summarizeSensitivityProfiles(clevelandSmall, sensitivity.measure='AUC_published')

RadioGx documentation built on Nov. 8, 2020, 8:21 p.m.