rectanglepy.tl.deconvolution¶
- rectanglepy.tl.deconvolution(signatures, bulks, correct_mrna_bias=True, n_cpus=None)¶
Performs recursive deconvolution using rectangle signatures and bulk data.
- Parameters:
signatures (RectangleSignatureResult) – The rectangle signature result containing the signature data and results.
bulks (pandas.DataFrame) – The tpm normalized bulk data for deconvolution. Rows are samples and columns are genes.
correct_mrna_bias (bool) – A flag indicating whether to correct for mRNA bias. Defaults to True.
n_cpus (int) – The number of CPUs to use for parallel processing. If not provided, the function will use all available CPUs. Each CPU will process a bulk sample.
- Return type:
DataFrame- Returns:
- -estimation_df (
DataFrame) A DataFrame containing the estimated cell fractions. Each row represents a sample, each column represents a cell type (including ‘Unknown’ if applicable).
- -bulk_err_df (
DataFrame) A DataFrame containing the gene-level difference between the true bulk expression and the reconstructed bulk expression (i.e.,
bulk - bulk_est) for each sample.
- -estimation_df (