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

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

Takes the sensitivity data from a RadioSet, and summarises them into a drug vs cell line table

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	'logical(1)' 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')

bhklab/RadioGx documentation built on Oct. 6, 2023, 8:27 a.m.