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.