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]