summarizeSensitivityProfiles {PharmacoGx} | R Documentation

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

### Description

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

### Usage

    summarizeSensitivityProfiles(pSet,
      sensitivity.measure = "auc_recomputed", cell.lines, drugs,
      summary.stat = c("mean", "median", "first", "last", "max", "min"),
      fill.missing = TRUE, verbose = TRUE)

### Arguments

`pSet` | [PharmacoSet] The PharmacoSet 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
`drugs` | `character` The drugs to be summarized. If any drugs 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, drugs across the columns, with the selected sensitivity statistic for each pair.

### Examples

    data(GDSCsmall)
    GDSCauc <- summarizeSensitivityProfiles(GDSCsmall, sensitivity.measure='auc_published')

[Package PharmacoGx version 1.14.2 Index]