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.

Return type:

AnnData

Parameters

DIANN_pathstr

Path to DIANN output file.

DIANN_sepstr, default ‘t’

Delimiter for DIANN output file.

metadata_pathOptional[str], default None

Path to metadata file.

metadata_sepstr, default ‘,’

Delimiter for metadata file.

metadata_filepath_headerstr, default ‘File.Name’

Name of the column in metadata file that contains the DIANN file paths.

filter_contaminationbool, default True

If True, removes Protein.Names labelled with ‘Cont_’ as a prefix.

filter_nan_genesbool, default True

If True, removes variable rows that contain NaN in the ‘Genes’ column.

n_of_protein_metadata_colsint, default 4

Number of protein metadata columns at the start of the DIANN file.

Returns:

AnnData

AnnData object with imported data.