summarizeMolecularProfiles-RadioSet-method: Takes molecular data from a RadioSet, and summarises them...

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

Takes molecular data from a RadioSet, and summarises them into one entry per drug

Description

Given a RadioSet with molecular data, this function will summarize the data into one profile per cell line, using the chosed summary.stat. Note that this does not really make sense with perturbation type data, and will combine experiments and controls when doing the summary if run on a perturbation dataset.

Usage

## S4 method for signature 'RadioSet'
summarizeMolecularProfiles(
  object,
  mDataType,
  cell.lines,
  features,
  summary.stat = c("mean", "median", "first", "last", "and", "or"),
  fill.missing = TRUE,
  summarize = TRUE,
  verbose = TRUE
)

Arguments

object	RadioSet The RadioSet to summarize
mDataType	character which one of the molecular data types to use in the analysis, out of all the molecular data types available for the rSet for example: rna, rnaseq, snp
cell.lines	character The cell lines to be summarized. If any cell.line has no data, missing values will be created
features	caracter A vector of the feature names to include in the summary
summary.stat	character which summary method to use if there are repeated cell.lines? Choices are "mean", "median", "first", or "last" In case molecular data type is mutation or fusion "and" and "or" choices are available
fill.missing	boolean should the missing cell lines not in the molecular data object be filled in with missing values?
summarize	A flag which when set to FALSE (defaults to TRUE) disables summarizing and returns the data unchanged as a ExpressionSet
verbose	boolean should messages be printed

Value

matrix An updated RadioSet with the molecular data summarized per cell line.

Examples

data(clevelandSmall)
clevelandSmall <- summarizeMolecularProfiles(clevelandSmall,
                    mDataType = "rna", cell.lines=sampleNames(clevelandSmall),
                    summary.stat = 'median', fill.missing = TRUE, verbose=TRUE)
clevelandSmall

bhklab/RadioGx documentation built on Oct. 6, 2023, 8:27 a.m.