getPerCellTypeDE: Do differential expression for each cell type in a conos...
In conos: Clustering on Network of Samples

getPerCellTypeDE

R Documentation

Do differential expression for each cell type in a conos object between the specified subsets of apps

Description

Do differential expression for each cell type in a conos object between the specified subsets of apps

Usage

getPerCellTypeDE(
  con.obj,
  groups = NULL,
  sample.groups = NULL,
  cooks.cutoff = FALSE,
  ref.level = NULL,
  min.cell.count = 10,
  remove.na = TRUE,
  max.cell.count = Inf,
  test = "LRT",
  independent.filtering = FALSE,
  n.cores = 1,
  cluster.sep.chr = "<!!>",
  return.details = TRUE
)

Arguments

`con.obj`	conos object
`groups`	factor specifying cell types (default=NULL)
`sample.groups`	a list of two character vector specifying the app groups to compare (default=NULL)
`cooks.cutoff`	boolean cooksCutoff for DESeq2 (default=FALSE)
`ref.level`	the reference level of the sample.groups against which the comparison should be made (default=NULL). If NULL, will pick the first one.
`min.cell.count`	integer Minimal number of cells per cluster for a sample to be taken into account in a comparison (default=10)
`remove.na`	boolean If TRUE, remove NAs from DESeq calculations, which often arise as comparisons not possible (default=TRUE)
`max.cell.count`	maximal number of cells per cluster per sample to include in a comparison (useful for comparing the number of DE genes between cell types) (default=Inf)
`test`	which DESeq2 test to use (options: "LRT" or "Wald") (default="LRT")
`independent.filtering`	boolean independentFiltering for DESeq2 (default=FALSE)
`n.cores`	numeric Number of cores (default=1)
`cluster.sep.chr`	character string of length 1 specifying a delimiter to separate cluster and app names (default='<!!>')
`return.details`	boolean Whether to return verbose details (default=TRUE)