Pseudobulk ccs for states

Compute a pseudobulk expression matrix for a ccs

pseudobulk_ccs_for_states(
  ccs,
  state_col = NULL,
  collapse_samples = FALSE,
  gene_group_df = NULL,
  agg_rowdata = NULL,
  cell_agg_fun = "mean",
  gene_agg_fun = "sum",
  norm_method = "size_only",
  scale_agg_values = FALSE,
  pseudocount = 0
)

Arguments

ccs

a cell count set object

state_col

column to aggregate expression. Defaults using the cell_group used in ccs construction.

collapse_samples

boolean Whether to collapse sample groups into one.

gene_group_df

A dataframe in which the first column contains gene ids or short gene names and the second contains group membership for creating metagene. If NULL, genes are not grouped.

agg_rowdata

A dataframe with metagene information, with the rows equal to the number of gene groupings. Must be specified if gene_group_df is not NULL. Otherwise this is ignored.