scReadSim.Utility.FeatureMapping

scReadSim.Utility.FeatureMapping(INPUT_bamfile, input_peaks, input_nonpeaks, output_peaks, output_nonpeaks, outdirectory, assignment_peak_file, assignment_nonpeak_file, n_top=50)[source]

Obtain mappings between input and output peaks, input and output non-peaks. The mappings are output as assignment_peak_file and assignment_nonpeak_file within outdirectory.

Parameters:

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

  • input_peaks (str) – BED file of user specified (or generated by scReadSim+MACS3) input peaks.

  • input_nonpeaks (str) – BED file of user specified (or generated by scReadSim+MACS3) input nonpeaks.

  • output_peaks (str) – BED file of user specified output peaks.

  • output_nonpeaks (str) – BED file of output non-peaks, generated by function ‘scATAC_CreateFeatureSets’.

  • outdirectory (str) – Output directory.

  • assignment_peak_file (str) – Specify the name of peak mapping file.

  • assignment_nonpeak_file (str) – Specify the name of nonpeak mapping file.

  • n_top ('int'(default: 50)) – Specify the number of input peaks (or non-peaks) with the most similar length as the candidate mapped input peaks (or non-peaks) for each the output peak (or non-peak). From the candidate input peaks (or non-peaks), scReadSim further selects the one with largest read density for peak mapping (smallest read density for non-peak mapping).