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ALLCools.clustering.incremental_pca

ALLCools.clustering.incremental_pca

Module Contents

_normalize_per_cell(matrix, cell_sum)[source]

Normalize matrix row sum to to cell_sum

class IncrementalPCA(n_components=100, sparse=False, normalize_per_cell=True, log1p=True, scale=True, **kwargs)[source]
fit(self, ds, use_cells=None, use_features=None, chunk=500000, cell_sum=None, var_dim='gene', obs_dim='cell', load_chunk=None, random_shuffle=True)[source]
transform(self, ds, use_cells=None, chunk=100000)[source]
fit_transform(self, ds, use_cells=None, use_features=None, chunk=500000, cell_sum=None, var_dim='gene', obs_dim='cell', load_chunk=None, random_shuffle=True)[source]

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