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Given metacells (usually from RNA data), project ATAC counts from multiple batches to get a McCounts object

Source: R/McCounts.R
scc_to_mcc_multi_batch.Rd

Given metacells (usually from RNA data), project ATAC counts from multiple batches to get a McCounts object

Usage

scc_to_mcc_multi_batch(
  scc_dirs,
  cell_to_metacell,
  ignore_metacells = c(-1, -2)
)

Arguments

scc_dirs

a vector of paths to directories containing ScCounts objects

cell_to_metacell

a data.frame with columns cell_id and metacell containing the mapping from single cell names to metacell names, or the name of an 'h5ad' file containing this information at the 'obs' slot. In such a case, the 'obs' slot should contain a column named metacell and the rownames should be the cell names.

ignore_metacells

a vector of metacells to ignore. Default: -1, -2 (the "outliers" metacell in the metacell2 python package).