subsetTo-RadioSet-method: A function to subset a RadioSet to data containing only...

In RadioGx: Analysis of Large-Scale Radio-Genomic Data

Description

This is the prefered method of subsetting a RadioSet. This function allows abstraction of the data to the level of biologically relevant objects: radiations and cells. The function will automatically go through all of the combined data in the RadioSet 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

## S4 method for signature 'RadioSet'
subsetTo(
  object,
  cells = NULL,
  radiationTypes = NULL,
  molecular.data.cells = NULL,
  keep.controls = TRUE,
  ...
)

Arguments

object	A RadioSet to be subsetted
cells	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.
radiationTypes	A list or vector of radiation names as used in the dataset to which the object will be subsetted. If left blank, then all radiationTypes will be left in the dataset.
molecular.data.cells	A list or vector of cell names to keep in the molecular data
keep.controls	If the dataset has perturbation type experiments, should the controls be kept in the dataset? Defaults to true.
...	Other arguments passed by other function within the package

Value

A RadioSet with only the selected radiation types and cells

Examples

clevelandRadiationTypes  <- radiationTypes(clevelandSmall)
clevelandCells <- cellNames(clevelandSmall)
RSet <- subsetTo(clevelandSmall, radiationTypes = clevelandRadiationTypes[1],
  cells = clevelandCells[1])
RSet

RadioGx documentation built on Nov. 8, 2020, 8:21 p.m.