getBetweenCellTypeDE: Compare two cell types across the entire panel

Description

Compare two cell types across the entire panel

Usage

getBetweenCellTypeDE(
  con.obj,
  groups = NULL,
  sample.groups = NULL,
  cooks.cutoff = FALSE,
  refgroup = NULL,
  altgroup = NULL,
  min.cell.count = 10,
  independent.filtering = FALSE,
  cluster.sep.chr = "",
  return.details = TRUE,
  only.paired = TRUE,
  remove.na = TRUE
)

Value

Returns either a DESeq2::results() object, or if return.details=TRUE, returns a list of the DESeq2::results(), the samples from the panel to use in this comparison, refgroups, altgroup, and samplegroups

Arguments

con.obj: conos object
groups: factor describing cell grouping (default=NULL)
sample.groups: a named list of two character vectors specifying the app groups to compare (default=NULL)
cooks.cutoff: boolean cooksCutoff parameter for DESeq2 (default=FALSE)
refgroup: cell type to compare to be used as reference (default=NULL)
altgroup: cell type to compare to be used as ALT against refgroup (default=NULL)
min.cell.count: numeric Minimum number of cells per celltype/sample combination to keep (default=10)
independent.filtering: boolean Whether to use independentFiltering parameter for DESeq2 (default=FALSE)
cluster.sep.chr: character string of length 1 specifying a delimiter to separate cluster and app names (default='<!!>')
return.details: boolean Return detailed results (default=TRUE)
only.paired: boolean Only keep samples that that both cell types above the min.cell.count threshold (default=TRUE)
remove.na: boolean If TRUE, remove NAs from DESeq calculations (default=TRUE)