protdata.io.read_diann

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protdata.io.read_diann#

protdata.io.read_diann(file, index_column='Protein.Group', sep='\\t')#

Load DIA-NN protein group matrix (report.pg_matrix.tsv) into an AnnData object.

Parameters:
file Union[str, DataFrame]

Path to DIA-NN report.pg_matrix.tsv file or a pandas DataFrame containing the data.

index_column str (default: 'Protein.Group')

Column name for protein group IDs.

sep str (default: '\\t')

File separator.

Return type:

AnnData

Returns:

anndata.AnnData object with:

  • X: intensity matrix (samples x proteins)

  • var: protein metadata (indexed by protein group IDs)

  • obs: sample metadata (indexed by sample names)

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