`root` and `leaves` with `test_association()`
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Hi, this is a great package, thank you.
in the test_association
documentation (https://scfates.readthedocs.io/en/latest/scFates.tl.test_association.html) it mentions there are optional root
and leaves
parameters to "restrain the test to a subset of the tree".
This looks like an association will be assessed for only the shortest root-to-tips path, is that correct?
When i try to use this I get an error:
e.g.
scf.tl.test_association(adata, leaves=[23,24], root=49)
>>>
`test_association() got an unexpected keyword argument 'leaves'`
When I inspect the source code for that function I can't see how one passes the root and leaves parameters either.
I can see there is a scf.tl.root() function to assign root, this seems like a good way to assign the root for ongoing analysis...but AFAICT there is no equiavlent function for leaves.
Any help would be gratefully received!
Hi @james-cranley,
root
and leaves
parameters have been removed from test_association
, the API documentation was not properly updated unfortunately, sorry for the confusion.
As there is no easy way to figure out later on whether the results from test_association
relate to the whole tree or a subset, function always run on the whole tree.
I would recommend to subset the tree before running test_association
using scf.tl.subset_tree
function, here is some information about how to use that function.
Thanks, Louis. I will try that route. Best, James.