hic3defdr.util.thresholding module

hic3defdr.util.thresholding.size_filter(clusters, cluster_size)[source]

Filters out clusters which are smaller than cluster_size.

Parameters:
  • clusters (list of set of tuple of int) – The clusters to filter.
  • cluster_size (int) – The minimum size of a cluster needed to pass this filter.
Returns:

The filtered clusters.
Return type:

list of set of tuple of int
hic3defdr.util.thresholding.threshold_and_cluster(qvalues, row, col, fdr)[source]

Thresholds pixels by comparing their q-values to a target FDR and clusters the significant and insignificant pixels.

Parameters:
  • qvalues (np.ndarray) – The qvalue for each pixel under consideration.
  • col (row,) – The row and column indices corresponding to the qvalues.
  • fdr (float) – The FDR to threshold on.
Returns:

sig_clusters, insig_clusters – Lists of the significant and insignificant clusters, respectively.
Return type:

list of set of tuple of int