stereo.io.read_gef

stereo.io.read_gef(file_path, bin_type='bins', bin_size=100, is_sparse=True, gene_list=None, region=None, gene_name_index=False, num_threads=-1)[source]

Read the GEF (.h5) file, and generate the StereoExpData object.

Parameters:

  • file_path (str) – the path to input file.

  • bin_type (str) – the bin type includes 'bins' or 'cell_bins'.

  • bin_size (int) – the size of bin to merge, which only takes effect when the bin_type is set as 'bins'.

  • is_sparse (bool) – the matrix is sparse matrix, if True, otherwise np.ndarray.

  • gene_list (Optional[list]) – select targeted data based on the gene list.

  • region (Optional[list]) – restrict data to the region condition, like [minX, maxX, minY, maxY].

  • gene_name_index (Optional[bool]) – True to set gene name as index if the version of gef file is 4 or greater, otherwise to set gene id, if the version is 3 or less, gene_name_index would be forced to True because there is no gene id in this case.

  • num_threads (int) – the number of threads to read the data, only available when bin_type is 'bins'. -1 means to use all the cores of the machine.

Return type:

An object of StereoExpData.