R/preprocessing_filtering_reduction.R
warning_raw_counts_to_sparse_matrix.RdWarning for raw_counts_to_sparse_matrix
warning_raw_counts_to_sparse_matrix( files_dir_list, file_type = c("scBAM", "scBED", "SparseMatrix"), peak_file = NULL, n_bins = NULL, bin_width = NULL, genebody = NULL, extendPromoter = 2500, verbose = TRUE, ref = "hg38" )
| files_dir_list | A named character vector of directory containing the raw files |
|---|---|
| file_type | Input file(s) type(s) ('scBED','scBAM','SparseMatrix') |
| peak_file | A file containing genomic location of peaks (NULL) |
| n_bins | The number of bins to tile the genome (NULL) |
| bin_width | The size of bins to tile the genome (NULL) |
| genebody | Count on genes (body + promoter) ? (NULL) |
| extendPromoter | If counting on genes, number of base pairs to extend up or downstream of TSS (2500). |
| verbose | Verbose (TRUE) |
| ref | reference genome to use (hg38) |
Error or warnings if the input are not correct