subsetTo: A function to subset a ToxicoSet to data containing only...

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

A function to subset a ToxicoSet to data containing only specified drugs, cells and genes

Description

This is the prefered method of subsetting a ToxicoSet. This function allows abstraction of the data to the level of biologically relevant objects: drugs and cells. The function will automatically go through all of the combined data in the ToxicoSet and ensure only the requested radiations and cell lines are found in any of the slots. This allows quickly picking out all the experiments for a radiation or cell of interest, as well removes the need to keep track of all the metadata conventions between different datasets.

Usage

subsetTo(
  object,
  cell_lines = NULL,
  drugs = NULL,
  molecular.data.cells = NULL,
  duration = NULL,
  features = NULL,
  ...
)

Arguments

object	A ToxicoSet to be subsetted
cell_lines	A list or vector of cell names as used in the dataset to which the object will be subsetted. If left blank, then all cells will be left in the dataset.
drugs	A list or vector of drug names as used in the dataset to which the object will be subsetted. If left blank, then all drugs will be left in the dataset.
molecular.data.cells	A list or vector of cell names to keep in the molecular data
duration	A list or vector of the experimental durations to include in the subset as strings. Defaults to all durations if parameter is not specified.
features	A list or vector of feature names as used in the dataset from which the object will be subsetted. If left blank that all features will be left in.
...	Other arguments passed to other functions within the package

Value

A ToxicoSet with only the selected drugs and cells

Examples

TGGATESDrugNames  <- treatmentNames(TGGATESsmall)
TGGATESCells <- sampleNames(TGGATESsmall)
tSet <- subsetTo(TGGATESsmall,drugs = TGGATESDrugNames[1],
  cells = TGGATESCells[1], duration = "2")

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