opendvp.io.DIANN_to_adata

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opendvp.io.DIANN_to_adata#

DIANN_to_adata(DIANN_path, DIANN_sep='\\t', metadata_path=None, metadata_sep=',', metadata_filepath_header='File.Name', filter_contamination=True, filter_nan_genes=True, n_of_protein_metadata_cols=4)#

Converts DIANN output file and metadata file into an AnnData object.

Parameters:

  • DIANN_path (str) – Path to DIANN output file.

  • DIANN_sep (str, default 't') – Delimiter for DIANN output file.

  • metadata_path (Optional[str], default None) – Path to metadata file.

  • metadata_sep (str, default ',') – Delimiter for metadata file.

  • metadata_filepath_header (str, default 'File.Name') – Name of the column in metadata file that contains the DIANN file paths.

  • filter_contamination (bool, default True) – If True, removes Protein.Names labelled with a Cont_ prefix.

  • filter_nan_genes (bool, default True) – If True, removes variable rows that contain NaN in the ‘Genes’ column.

  • n_of_protein_metadata_cols (int, default 4) – Number of protein metadata columns at the start of the DIANN file.

Returns:

AnnData object with imported data.

Return type:

anndata.AnnData

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