scReadSim.GenerateSyntheticCount.scATAC_GenerateSyntheticCount_MultiSample

scReadSim.GenerateSyntheticCount.scATAC_GenerateSyntheticCount_MultiSample(INPUT_bamfile, outdirectory, n_cell_new=None, total_count_new=None, n_cluster=None, n_cores=1)[source]

Multi-sample/replicate implement of scReadSim for simulating scATAC-seq synthetic count matrix.

Parameters:

  • INPUT_bamfile (str) – List of input BAM files (use absolute paths to the BAM files).

  • outdirectory (str) – Specify the working directory of scReadSim for generating intermediate and final output files.

  • 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.

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