DEA.permutateClones: DEA.permutateClones

In plger/iPSCpoweR: iPSCpoweR: transcriptomics-based evaluation of experimental designs for iPSC disease modeling

Description

Performs differential-expression analyses between groups constituted by corresponding iPSC clones from random individuals (for each individual, one clone is randomly assigned to one group, and the other to the second group).

Usage

DEA.permutateClones(
  nbIndividuals = 2,
  maxTests = 50,
  res = NULL,
  seed = 1,
  addDE = F,
  addDE.foldchanges = c(1.25, 1.5, 2, 3, 5),
  addDE.nbPerFC = 10,
  paired = F,
  doSave = T,
  returnResults = F,
  ncores = NULL,
  quiet = F,
  filter = NULL,
  useExactTest = T,
  DEAfunc = edgeRwrapper
)

Arguments

nbIndividuals	A positive integer indicating the number of individuals to consider (default 2).
maxTests	The maximum number of tests to run (default 50).
res	The result of 'aggByClone(getGeneExpr())', optional and used only to speed up multiple calls or use a custom dataset.
seed	The seed (for randomization)
addDE	Logical; whether to add random differentially-expressed genes (default FALSE).
addDE.foldchanges	A numeric vector of foldchanges to add (will use the given foldchanges and their inverse). Default c(1.1,1.25,1.5,2,3,5).
addDE.nbPerFC	The number of DEGs for each foldchange (default 5).
paired	Logical; whether to run the analysis in a paired way, i.e. '~individual+group' (default FALSE).
doSave	Whether to save the results (default TRUE).
returnResults	Whether to return the results (default FALSE).
ncores	Integer; number of cores to use. Defaults to detected number of cores minus one.
quiet	Logical; if TRUE, suppresses progress report (default FALSE)
filter	Function; the filter for genes to be tested, to be applied to all rows of the expression matrix (default: no filter). An example value for the filter argument would be ‘sum(x>10)>2’, which would only include genes that have more than 10 counts in more than 2 samples.
useExactTest	Logical; whether to use edgeR's exact test for unpaired analysis. Works only with DEAfunc=edgeRwrapper.
DEAfunc	Function; the function used to run the differential expression analysis (by default, the ‘edgeRwrapper’ function of this package).

Value

Nothing (results save to files), or a data.frame if returnResults=TRUE.

plger/iPSCpoweR documentation built on Feb. 2, 2022, 1:37 a.m.