scReadSim.Utility.scATAC_bam2countmat_OutputPeak

scReadSim.Utility.scATAC_bam2countmat_OutputPeak(cells_barcode_file, assignment_file, INPUT_bamfile, outdirectory, count_mat_filename)[source]

Construct count matrix for task with user input features set.

Parameters:

  • cells_barcode_file (str) – Cell barcode file corresponding to the input BAM file.

  • assignment_file (str) – Features mapping file output by function Utility.FeatureMapping.

  • INPUT_bamfile (str) – Input BAM file for anlaysis.

  • outdirectory (str) – Specify the output directory of the count matrix file.

  • count_mat_filename (str) – Specify the base name of output count matrix.