pycallingcards.tools.footprint#

pycallingcards.tools.footprint(peak_data, qbed_data, fixed_number=50, compress_number=0, min_insertions=15, delete_unfound=False, resultname=['Chr_footprint', 'Start_footprint', 'End_footprint'], return_bed=False)[source]#

Find the CC footprint in yeast CC data.

Parameters:

  • peak_data (DataFrame) – pd.DataFrame of the peak data with the first three columns as chromosome, start and end.

  • qbed_data (DataFrame) – pd.DataFrame of the qbed data where peaks are called from.

  • fixed_number (float (default: 50)) – The minimum length of a footprint.

  • compress_number (float (default: 0)) – How many standard deviation should the footprint conpress. The larger compress_number, the shorter the footprint is.

  • min_insertions (int (default: 15)) – Minimum insertion numbers for the algorithm to start.

  • delete_unfound (bool (default: False)) – If False, the point that is not a footprint point will keep the original start and end sites. If True, the point that is not a footprint point will be [None,None,None].

  • resultname (list (default: ['Chr_footprint', 'Start_footprint', 'End_footprint'])) – The column name of the final results.

  • return_bed (bool (default: False)) – If False, the function will return the footprint result to the end columns of the data. If True, the function will return only the footprint results and delete all the none columns.

Example:

Please check `tutorial <https://pycallingcards.readthedocs.io/en/latest/tutorials/notebooks/yeast.html>`for details.

Return type:

DataFrame