getBetweenCellTypeCorrectedDE {conos}

Compare two cell types across the entire panel

Description

Compare two cell types across the entire panel

Usage

getBetweenCellTypeCorrectedDE(
  con.obj,
  sample.groups = NULL,
  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,
  correction = NULL,
  ref.level = NULL
)

Arguments

con.obj

conos object

sample.groups

a named list of two character vectors specifying the app groups to compare

groups

factor describing cell grouping

cooks.cutoff

cooksCutoff parameter for DESeq2

refgroup

cell type to compare to be used as reference

altgroup

cell type to compare to

min.cell.count

minimum number of cells per celltype/sample combination to keep

independent.filtering

independentFiltering parameter for DESeq2

cluster.sep.chr

character string of length 1 specifying a delimiter to separate cluster and app names

return.details

logical, return detailed results

only.paired

only keep samples that that both cell types above the min.cell.count threshold

correction

fold change corrections per genes

ref.level

reference level on the basis of which the correction was calculated

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