Open timothymillar opened 1 year ago
@jeromekelleher suggests also adding "Pedigree statistics" top level section to the documentation https://github.com/pystatgen/sgkit/issues/1025#issuecomment-1436755539.
I was actually just looking for documentation this morning answering a question about computing inbreeding from simulations
Could you give some more detail on these simulations?
Discussion here: https://github.com/tskit-dev/tskit/discussions/2711
This is mostly covered by #1072, but I might leave it open for now as I think there is room for more pedigree specific documentation.
We don't currently have any IO functionality for pedigree formats. These are usually tabular but can be quite variable. We should document how to read in some generic examples and add them to an sgkit style dataset.
Basic workflow:
sample_id
variableparent_id
variableparents
dim (['Father', 'Mother']
,['Sire', 'Dam']
, etc.)parent_indices
to generate theparents
array and explain the 0-based indexing etc.