summarizeSensitivityProfiles: 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

summarizeSensitivityProfiles(rSet,
  sensitivity.measure = "AUC_recomputed", cell.lines, radiation.types,
  summary.stat = c("mean", "median", "first", "last", "max", "min"),
  fill.missing = TRUE, verbose = TRUE)

Arguments

rSet	[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(Cleveland_small)
GDSCauc <- summarizeSensitivityProfiles(Cleveland_small, sensitivity.measure='AUC_published')

RadioGx documentation built on Dec. 20, 2019, 1:06 a.m.