getBetweenCellTypeDE {conos}

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
)

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)

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