scReadSim.GenerateSyntheticCount.scATAC_GenerateSyntheticCount

scReadSim.GenerateSyntheticCount.scATAC_GenerateSyntheticCount(count_mat_filename, directory, outdirectory, doub_classification_label_file=None, n_cell_new=None, total_count_new=None, celllabel_file=None, n_cluster=None, n_cores=1)[source]

Simulate synthetic count matrix.

Parameters:

  • count_mat_filename (str) – Base name of the count matrix output by function bam2countmat().

  • directory (str) – Path to the count matrix.

  • outdirectory (str) – Output directory of coordinate files.

  • doub_classification_label_file (str) – Specify the absolute path to the doublet classification result doublet_classification.Rdata.

  • n_cell_new (int (default: None)) – Number of synthetic cells. If not specified, scReadSim uses the number of real cells.

  • total_count_new (int (default: None)) – Number of (expected) sequencing depth. If not specified, scReadSim uses the real sequencing depth.

  • celllabel_file (str (default: None)) – Specify the one-column text file containing the predefined cell labels. Make sure that the order of cell labels correspond to the cell barcode file (and the columns of real count matrix). If no cell labels are specified, scReadSim performs a Louvain clustering before implementing scDesign2.

  • n_cores (int (default: 1)) – Number of cores for parallel computing.