merquaco.data_loss.DropoutResult.get_considered_genes

DropoutResult.get_considered_genes(fov: str = '', dic: bool = False)

Gets a list of all genes with at least 1 FOV considered for dropout. FOV is considered for dropout only if its 4 carinal neighbors average at least 100 transcripts. If fov is specified, returns list for the specified FOV. If dic=True, returns a dictionary of considered genes for each considered FOV.

Parameters:

  • fov (str, optional) – FOV for which to get list of considered genes. Default is ‘’.

  • dic (bool, optional) – Whether to return dictionary of considered genes for each considered FOV. Default is False.

Returns:

  • list – If fov is specified. List of considered genes for that FOV.

  • dict – If dic is True. Dictionary of considered genes per considered FOV

  • list – If all arguments are default. List of genes with at least one considered FOV.