Model Changes in Celltype Frequencies with Dirichlet Multinomial Regression

Model Changes in Celltype Frequencies with Dirichlet Multinomial Regression

model_celltype_freqs(
  sce,
  unique_id_var = "manifest",
  celltype_var = "cluster_celltype",
  dependent_var = "group",
  ref_class = "Control",
  var_order = NULL,
  confounding_vars = NULL,
  ...
)

Arguments

sce

a SingleCellExperiment object

unique_id_var

the unique identifier variable for each sample

celltype_var

the colData variable specifying celltype or subtype

dependent_var

the name of the colData variable for contrasts

ref_class

the class of dependent_var used as reference

var_order

Optional re-ordering of subset_group factor levels. Default NULL.

confounding_vars

Additional confounding variables from colData.

...

Additional arguments

Value

results_l a list of results

See also

Other Celltype annotation: find_marker_genes(), map_celltypes_sce()