getBetweenCellTypeCorrectedDE: Compare two cell types across the entire panel

In conos: Clustering on Network of Samples

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

conos documentation built on May 29, 2024, 9:56 a.m.