ToxicoGx (version 0.1.1)

rankGeneDrugPerturbation: Rank genes based on drug effect

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