rankGeneDrugPerturbation: Rank genes based on drug effect

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

Description

A helper function called from within 'drugPerturbationSig'. This is intended for developer use only; if you aren't debugging the package, this should not be used.

Usage

rankGeneDrugPerturbation(
  data,
  drug,
  drug.id,
  drug.concentration,
  type,
  xp,
  batch,
  duration,
  single.type = FALSE,
  nthread = 1,
  verbose = FALSE
)

Arguments

data:	gene expression data matrix
drug:	single or vector of drug(s) of interest; if a vector of drugs is provided, they will be considered as being the same drug and will be jointly analyszed
drug.id:	drug used in each experiment
drug.concentration:	drug concentration used in each experiment
type:	cell or tissue type for each experiment
xp:	type of experiment (perturbation or control)
batch:	experiment batches
duration:	The duration of the experiment, in a consistent unit
single.type:	Should the statitsics be computed for each cell/tissue type separately?
nthread:	number of parallel threads (bound to the maximum number of cores available)

Value

[list] of data.frames with the statistics for each gene, for each type

ToxicoGx documentation built on Jan. 20, 2020, 5:06 p.m.