summarizeSensitivityProfiles {ToxicoGx} | R Documentation

## 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')

[Package ToxicoGx version 1.4.0 Index]