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Thanks for developing such a useful tool for reconstructing phylogenetic tree. when looking into the source code of assigning lineage groups to each cells, I am not sure about if it is correct in several details. There are two main questions confusing me as follows:
the above intBC set was used in iteratively assignment of lineage groups and the bottom one master_intBC was applied to calculate kinship_score. but these two intBC sets were actually not same because they were filtered via different criteria. so I am wondering if it is more efficient and accurate than using the same criteria to selecting intBC set and master_intBC?
Hope I have got the meaning of your code and looking forward to your reply~
The text was updated successfully, but these errors were encountered:
AmoriLi
changed the title
issues about assidgn_lineage_groups() function
issues about assign_lineage_groups() function
Nov 23, 2022
Thanks for developing such a useful tool for reconstructing phylogenetic tree. when looking into the source code of assigning lineage groups to each cells, I am not sure about if it is correct in several details. There are two main questions confusing me as follows:
https://github.com/YosefLab/Cassiopeia/blob/master/cassiopeia/preprocess/lineage_utils.py
![Screen Shot 2022-11-23 at 12 01 02 AM](https://user-images.githubusercontent.com/80192100/203362123-1efae477-78bc-48a8-b2c4-c9c511abfde5.png)
1.
in the last 3rd line, should it be 'prev_clust_size = piv_nolg.shape[0]' because we only need to assign lineage group to the undefined cells with number more than 'min_clust_size'. Is there something important I've missed or misunderstood?
the above intBC set was used in iteratively assignment of lineage groups and the bottom one master_intBC was applied to calculate kinship_score. but these two intBC sets were actually not same because they were filtered via different criteria. so I am wondering if it is more efficient and accurate than using the same criteria to selecting intBC set and master_intBC?
Hope I have got the meaning of your code and looking forward to your reply~
The text was updated successfully, but these errors were encountered: