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schicluster.loop.loop_bkg

schicluster.loop.loop_bkg#

Module Contents#

calc_diag_stats(E, n_dims)[source]#

Calculate cutoff, average, std, count of non-zero pixels of each diagonals of the E

calculate_chrom_background_normalization(cell_url, chrom, resolution, output_prefix, dist=5050000, cap=5, pad=5, gap=2, min_cutoff=1e-06, log_e=False, shuffle=False)[source]#

Compute the background for each chromosome in each cell

Parameters:

  • cell_url –

  • chrom –

  • resolution –

  • output_prefix –

  • dist –

  • cap –

  • pad –

  • gap –

  • min_cutoff –

  • log_e –

  • shuffle –

Returns:

  • E is the global diagonal normalized matrix

  • T is the local background normalized version of E

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