getPerCellTypeDE: 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
)

Value

A list of differential expression results for every cell type

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)