iced.filter.filter_low_counts¶

iced.filter.filter_low_counts(X, lengths=None, percentage=0.02, copy=True, sparsity=True, remove_all_zeros_loci=False, verbose=False)¶

Filter rows and columns with low counts

Parameters:

X : ndarray (n, n) Count matrix (hollow, symetric) lengths : ndarray (m, ), optional, default: None Lengths of the chromosomes percentage : float, optional, default: 0.02 percentage of rows and columns to discard remove_all_zeros_loci : bool, optional, default: False if set to True, the filtering will remove first all the non interacting loci, and then apply the filtering strategy chosen. copy : boolean, optional, default: True If set to true, copies the count matrix sparsity : boolean, optional, default: True Whether to use the sparsity of the region or the total number of counts of the region to filer.