summarizeMolecularProfiles: Takes molecular data from a ToxicoSet, and summarises them...

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

Takes molecular data from a ToxicoSet, and summarises them into one entry per drug and experimental condition.

Description

Given a ToxicoSet with molecular data, this function will summarize the data into one profile per experimental condition (duration, dose level) using the chosen summary.stat and return a SummarizedExperiment object, with one Assay corresponding to a requested drug.

Usage

summarizeMolecularProfiles(
  tSet,
  mDataType,
  cell_lines = NULL,
  drugs = NULL,
  features = NULL,
  duration = NULL,
  dose = c("Control", "Low", "Middle", "High"),
  summary.stat = c("mean", "median", "first", "last"),
  fill.missing = TRUE,
  summarize = TRUE,
  verbose = TRUE
)

Arguments

tSet	ToxicoSet The ToxicoSet 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 tSet for example: rna
cell_lines	character The cell lines to be summarized. If any cell.line has no data, missing values will be created
drugs	character The drugs to be summarized
features	character A vector of the feature names to include in the summary
duration	character A vector of durations to summarize across
dose	character The dose level to summarize replicates across
summary.stat	character which summary method to use if there are repeated cell_lines? Choices are "mean", "median", "first", or "last"
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

SummarizedExperiment A SummarizedExperiment object with the molecular data summarized per cell line.

Examples

data(TGGATESsmall)
summMP <- ToxicoGx::summarizeMolecularProfiles(
  tSet = TGGATESsmall, mDataType = "rna",
  cell_lines=sampleNames(TGGATESsmall), drugs = head(treatmentNames(TGGATESsmall)),
  features = fNames(TGGATESsmall,"rna")[seq_len(100)], duration = "8",
  dose = c("Control", "High"), summary.stat = "median",
  fill.missing = TRUE, verbose=TRUE
  )

#subset into expression matrix for a requested drug
assays <- SummarizedExperiment::assays(summMP)[[treatmentNames(TGGATESsmall)[1]]]
#summarization of phenoData for requested experiments
phenoData <- SummarizedExperiment::colData(summMP)
#summarization of phenoData for requested experiments
featureData <- SummarizedExperiment::rowData(summMP) #featureData for requested experiments

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