DEA.permutateIndividuals: DEA.permutateIndividuals

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

Description

Performs differential-expression analyses between samples from random individuals.

Usage

DEA.permutateIndividuals(
  nbIndividuals = 2,
  maxTests = 50,
  nbClone = 2,
  res = NULL,
  useOnlyMulticlone = TRUE,
  seed = 1,
  addDE = FALSE,
  addDE.foldchanges = c(1.25, 1.5, 2, 3, 5),
  addDE.nbPerFC = 10,
  doSave = TRUE,
  returnResults = !doSave,
  ncores = NULL,
  quiet = FALSE,
  filter = function(x) sum(x > 10) > 2,
  nested = FALSE,
  fasterCombinations = TRUE,
  DEAfunc = edgeRwrapper
)

Arguments

nbIndividuals	Either a positive integer, or a vector of positive integers of length 2, indicating the number of individuals in each group (default 2).
maxTests	The maximum number of tests to run (default 50).
nbClone	The number of iPSC clones to consider from each individual (default 2)
res	The dataset to use. Should be a list with two slots ('annotation' and 'dat'), as the object available in 'data("GSE79636")'. If left NULL, the HipSci dataset is automatically fetched and aggregated (to avoid doing this everything when calling the function with different designs, first run 'aggByClone(getGeneExpr())' and pass its result via this argument.
useOnlyMulticlone	Logical; whether to use only the samples that have more than one clone (default TRUE). Disabling this greatly increase the number of possible combinations, but will make the search for viable combinations _very_ slow. It should be used only if insufficient viable combinations are available (e.g. for nbIndividuals > 5).
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, applied on the first group).
addDE.nbPerFC	The number of DEGs for each foldchange.
doSave	Whether to save the results (default TRUE).
returnResults	Whether to return the results (default FALSE unless 'doSave=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.
nested	Logical; whether to run the analysis using duplicateCorrelation (default FALSE). Requires 'nbClone=2' and 'DEAfunc=voomWrapper'.
fasterCombinations	Logical; whether to find combinations rapidly by selecting a pre-defined sex ratio (default FALSE). Useful for large datasets.
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.