radSensitivitySig: Creates a signature representing the association between gene...

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

Creates a signature representing the association between gene expression (or other molecular profile) and radiation dose response, for use in radiation sensitivity analysis.

Description

Given a RadioSet of the sensitivity experiment type, and a list of radiation types, the function will compute a signature for the effect of gene expression on the molecular profile of a cell. The function returns the estimated coefficient, the t-stat, the p-value and the false discovery rate associated with that coefficient, in a 3 dimensional array, with genes in the first direction, drugs in the second, and the selected return values in the third.

Usage

radSensitivitySig(
  rSet,
  mDataType,
  radiation.types,
  features,
  sensitivity.measure = "AUC_recomputed",
  molecular.summary.stat = c("mean", "median", "first", "last", "or", "and"),
  sensitivity.summary.stat = c("mean", "median", "first", "last"),
  returnValues = c("estimate", "pvalue", "fdr"),
  sensitivity.cutoff = NA,
  standardize = c("SD", "rescale", "none"),
  nthread = 1,
  verbose = TRUE,
  ...
)

Arguments

rSet	A RadioSet of the perturbation experiment type
mDataType	character which one of the molecular data types to use in the analysis, out of dna, rna, rnaseq, snp, cnv
radiation.types	character a vector of radiation.types for which to compute the signatures. Should match the names used in the PharmacoSet.
features	character a vector of features for which to compute the signatures. Should match the names used in correspondant molecular data in PharmacoSet.
sensitivity.measure	character which measure of the radiation sensitivity should the function use for its computations? Use the sensitivityMeasures function to find out what measures are available for each PSet.
molecular.summary.stat	What summary statistic should be used to summarize duplicates for cell line molecular profile measurements?
sensitivity.summary.stat	What summary statistic should be used to summarize duplicates for cell line sensitivity measurements?
returnValues	character Which of estimate, t-stat, p-value and fdr should the function return for each gene?
sensitivity.cutoff	Allows to provide upper and lower bounds to sensitivity measures in the cases where the values exceed physical values due to numerical or other errors.
standardize	character One of "SD", "rescale", or "none", for the form of standardization of the data to use. If "SD", the the data is scaled so that SD = 1. If rescale, then the data is scaled so that the 95 interquantile range lies in [0,1]. If none no rescaling is done.
nthread	numeric if multiple cores are available, how many cores should the computation be parallelized over?
verbose	boolean 'TRUE' if the warnings and other infomrative message shoud be displayed
...	additional arguments not currently fully supported by the function

Value

list a 3D array with genes in the first dimension, radiation.types in the second, and return values in the third.

Examples

data(clevelandSmall)
rad.sensitivity <- radSensitivitySig(clevelandSmall, mDataType="rna",
             nthread=1, features = fNames(clevelandSmall, "rna")[1],
             radiation.types=treatmentNames(clevelandSmall))
print(rad.sensitivity)

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