grassp.io.read_fragpipe

read_fragpipe(*args, **kwargs)

Read FragPipe combined_protein.tsv file into an AnnData object.

This function serves as a wrapper around read_fragpipe(), automatically transposing the data so that proteins are stored in .obs (rows) and samples in .var (columns), following grassp conventions.

Parameters:

*args

Positional arguments passed to protdata.io.read_fragpipe().

**kwargs

Keyword arguments passed to protdata.io.read_fragpipe().

Return type:

AnnData

Returns:

AnnData Annotated data object with proteins as observations (rows) and samples as variables (columns).

See also

protdata.io.read_fragpipe

Original protdata function for reading FragPipe files.

Examples

>>> import grassp as gr
>>> adata = gr.io.read_fragpipe('combined_protein.tsv')