This function will return a sparse matrix of
length(cell_indices_ls) x number of genes (in list form in CSR).
The function has the option to return the sum of the sum of the raw counts
or the average of the normalised counts.
Usage
rs_pseudobulk_cells_sparse(f_path, cell_indices_ls, assay, verbose)
Arguments
- f_path
String. Path to the counts_cells.bin file.
- cell_indices_ls
List. Must contains 0-indexed positions of the
cells to aggregate per element.
- assay
String. One of c("raw", "norm"). Which counts to normalise.
- verbose
Controls verbosity of the function
Value
A list with the following elements (easy to convert into CSR in R)
indptr - The index pointers (representing cells)
indices - The indices (representing genes)
data - The pseudo-bulked data
nrow - Number of rows (i.e., pseudo-bulked samples)
ncol - Number of columns