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

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

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

## S4 method for signature 'PharmacoSet'
summarizeSensitivityProfiles(
  object,
  sensitivity.measure = "auc_recomputed",
  cell.lines,
  profiles_assay = "profiles",
  treatment_col = "treatmentid",
  sample_col = "sampleid",
  drugs,
  summary.stat = c("mean", "median", "first", "last", "max", "min"),
  fill.missing = TRUE,
  verbose = TRUE
)

Arguments

object	PharmacoSet The PharmacoSet from which to extract the data
sensitivity.measure	character The sensitivity measure to use. Use the sensitivityMeasures function to find out what measures are available for each object.
cell.lines	character The cell lines to be summarized. If any cell lines have no data, they will be filled with missing values.
profiles_assay	character The name of the assay in the PharmacoSet object that contains the sensitivity profiles.
treatment_col	character The name of the column in the profiles assay that contains the treatment IDs.
sample_col	character The name of the column in the profiles assay that contains the sample IDs.
drugs	character The drugs to be summarized. If any drugs have no data, they will be filled with missing values.
summary.stat	character The summary method to use if there are repeated cell line-drug experiments. Choices are "mean", "median", "first", "last", "max", or "min".
fill.missing	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')

bhklab/PharmacoGx documentation built on April 18, 2024, 3:13 a.m.