scReadSim.scATAC_GenerateBAM.scATAC_CombineBED

scReadSim.scATAC_GenerateBAM.scATAC_CombineBED(outdirectory, peak_read_bedfile_prename, nonpeak_read_bedfile_prename, BED_filename_combined_pre, GrayAreaModeling=True)

Combine the bed files of foreground and background feature sets into one bed file.

Parameters:

• outdirectory (str) – Directory of peak_read_bedfile_prename.txt and nonpeak_read_bedfile_prename.txt.

• peak_read_bedfile_prename (str) – Base name of the bed file containig synthetic reads for peaks (generated by function scATAC_GenerateBAM.scATAC_GenerateBAMCoord).

• nonpeak_read_bedfile_prename ('str') – Base name of the bed file containig synthetic reads for non-peaks (generated by function scATAC_GenerateBAM.scATAC_GenerateBAMCoord).

• BED_filename_combined_pre ('str') – Specify the combined syntehtic reads bed file prename. The combined bed file will be output to outdirectory.

• GrayAreaModeling (bool (default: ‘True’)) – Specify whether to combine gray area’s reads.