protdata.io.read_fragpipe

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protdata.io.read_fragpipe#

protdata.io.read_fragpipe(file, intensity_column_suffixes=[' MaxLFQ Intensity', ' Spectral Count', ' Unique Spectral Count'], index_column='Protein ID', sep='\\t')#

Load a FragPipe protein group matrix into an AnnData object.

Parameters:
file Union[str, DataFrame]

Path to the FragPipe combined_protein.tsv file or a pandas DataFrame containing the data.

intensity_column_suffixes default: [' MaxLFQ Intensity', ' Spectral Count', ' Unique Spectral Count']

Suffix(es) for intensity columns to extract. The first suffix is used for the main matrix (X), others are stored as layers if present.

index_column str (default: 'Protein ID')

Column name to use as protein index.

sep str (default: '\\t')

File separator if reading from file.

Return type:

AnnData

Returns:

anndata.AnnData object with:

  • X: intensity matrix (samples x proteins)

  • var: protein metadata (indexed by protein IDs)

  • obs: sample metadata (indexed by sample names)

  • layers: additional intensity matrices if multiple intensity column suffixes are provided

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