pycallingcards.plotting.calculate_signal#

pycallingcards.plotting.calculate_signal(peak_data, chipseq_signal, before=10000, after=10000, signaltype='mean', nbins=100)[source]#

Calculate the matrix of Chip-seq signal in each peak. This function uses pyBigWig, please install it before using.

Parameters:

  • peak_data (DataFrame) – Peak_data file from cc.pp.callpeaks.

  • chipseq_signal (str) – Chipseq signal file should be bigWig/bigBed file.

  • before (int (default: 10000)) – The length(bp) calculated before the middle point of the peak.

  • after (int (default: 10000)) – The length(bp) calculated after the middle point of the peak.

  • signaltype (Optional[Literal['mean', 'median', 'min', 'max', 'sum', 'std']] (default: 'mean')) – [‘mean’, ‘median’, ‘min’, ‘max’, ‘sum’ ,’std’]. Define the type of statistic to be used over the bin size range.

  • nbins (int (default: 100)) – The number of bins calculated.

Example:

>>> import pycallingcards as cc
>>> exp_ccf = cc.datasets.SP1_K562HCT116_data(data = 'HCT116_SP1_ccf')
>>> bg_ccf = cc.datasets.SP1_K562HCT116_data(data = 'HCT116_brd4_ccf')
>>> peak_data = cc.pp.callpeaks(exp_ccf, bg_ccf, method = 'ccf_tools', reference = 'hg38', pvalue_cutoffbg = 0.0001, window_size = 2000, step_size = 500,
          pvalue_cutoffTTAA = 0.0000001, lam_win_size = None)
>>> # If "https://www.encodeproject.org/files/ENCFF587ZMX/@@download/ENCFF587ZMX.bigWig" could not work, please download it and read the local path.
>>> mtx = cc.pl.calculate_signal(peak_data,"https://www.encodeproject.org/files/ENCFF587ZMX/@@download/ENCFF587ZMX.bigWig")