summarizeSensitivityProfiles: Takes the sensitivity data from a ToxicoSet, and summarises...

In bhklab/ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

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

Description

This function creates a table with drug as rows and cell lines as columns, summarising the drug senstitivity data of a ToxicoSet into drug-cell line pairs for a specified experiment duration.

Usage

summarizeSensitivityProfiles(
  tSet,
  duration = NULL,
  cell_lines = NULL,
  drugs = NULL,
  sensitivity.measure = "auc_recomputed",
  summary.stat = c("mean", "median", "first", "last", "max", "min"),
  fill.missing = TRUE,
  verbose = TRUE
)

Arguments

tSet	ToxicoSet The ToxicoSet from which to extract the data
duration	numeric The duration at which to summarize the drug-cell combo. This is a required parameter.
cell_lines	character The cell lines to be summarized. If any cell lines has no data, it will be filled with missing values
drugs	character The drugs to be summarized. If any drugs has no data, it will be filled with missing values. Defaults to include all drugs in the given tSet.
sensitivity.measure	character which sensitivity sensitivity.measure to use? Use the sensitivityMeasures function to find out what measures are available for each TSet.
summary.stat	character which summary method to use if there are repeated cell line-drug experiments? Choices are "mean", "median", "first", "last", "max", or "min"
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 drugs going down the rows, cell lines across the columns, with the selected sensitivity statistic for each pair.

Examples

data(TGGATESsmall)
TGGATESauc <- summarizeSensitivityProfiles(TGGATESsmall, sensitivity.measure='auc_recomputed')

bhklab/ToxicoGx documentation built on March 18, 2023, 6:44 a.m.