how can I map my cells to an previously generated cluster? about bnpc

[NBMueller]

Hey,

Currently, there is only the argument --fixed_assignment <ASSIGNMENT FILE> implemented, which does not update cluster assignments, but that is not what you want, is it?

As I understand (I did not get your example fully), you want to have the assignment flexible/learned but the clusters fixed?
You could do the same as for the assignment, init the clusters from a given file, and then just update the assignments and skip the rest of the update steps (https://github.com/cbg-ethz/BnpC/blob/b4dfefc1962b4802ab685604d321548035456e6e/libs/MCMC.py#LL321C27-L321C27).

Unfortunately, I don't have the time atm to implement it myself, but let me know if you get stuck somewhere.

Cheers

[jeffchen2000]

Great, thank you so much! I will try and let you know. Again, thanks a lot. Xianfeng Chen From: Nico B. ***@***.***> Sent: Monday, May 22, 2023 1:51 AM To: cbg-ethz/BnpC ***@***.***> Cc: Chen, Xianfeng, Ph.D. ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [cbg-ethz/BnpC] how can I map my cells to an previously generated cluster? (Issue #27) Hey, Currently, there is only the argument --fixed_assignment <ASSIGNMENT FILE> implemented, which does not update cluster assignments, but that is not what you want, is it? As I understand (I did not get your example fully), you want to have the assignment flexible/learned but the clusters fixed? You could do the same as for the assignment, init the clusters from a given file, and then just update the assignments and skip the rest of the update steps (https://github.com/cbg-ethz/BnpC/blob/b4dfefc1962b4802ab685604d321548035456e6e/libs/MCMC.py#LL321C27-L321C27). Unfortunately, I don't have the time atm to implement it myself, but let me know if you get stuck somewhere. Cheers - Reply to this email directly, view it on GitHub<#27 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJLCGDO2BY5PAGLMPTEVBADXHMSILANCNFSM6AAAAAAYATPDKA>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[jeffchen2000]

hi Bnpc team seems --fixed_assignment <ASSIGNMENT FILE> implemented is not what I want. I want the cluster and mutation to be fixed like below (this can be from another study, and they detected 5 clusters), now, I want to map my sample cells to the fixed clusters mutation_ID cluster1 cluster2 cluster3 cluster4 cluster5 13_32893245_._A_G,C 0 0 0 0 0 13_32906729_._A_C,T 1 0 1 1 1 13_32907171_._G_T,A 0 0 0 0 0 13_32907303_._GGCC_AGCC,* 0 0 0 0 0 13_32907305_._C_A,T 0 0 0 0 0 13_32907306_._C_A,T 0 0 0 0 0 13_32907420_._GA_G,AA 0 0 0 0 0 13_32911073_._CA_C,TA 0 0 0 0 0 13_32911873_._T_A,C 0 0 0 0 0 13_32912175_._A_G,C 0 0 0 0 0 13_32912345_._GA_G,AA 0 0 0 0 0 13_32912472_._C_T,A 0 0 0 0 0 13_32912674_._A_G,T 0 0 0 0 0 13_32913558_._CA_C,TA 0 0 0 0 0 And after mapping, I expect to get "genotypes_posterior_mean.tsv" as below (where each column is each of my cells, each of my cell is assigned to the cluster of the (cluster1-5 above) cluster1 Cluster2 Cluster3 cluster1 cluster1 cluster1 cluster1 13_32893245_._A_G,C 0 0 0 0 0 0 0 13_32906729_._A_C,T 1 0 1 1 1 1 0 13_32907171_._G_T,A 0 0 0 0 0 0 0 13_32907303_._GGCC_AGCC,* 0 0 0 0 0 0 0 13_32907305_._C_A,T 0 0 0 0 0 0 0 13_32907306_._C_A,T 0 0 0 0 0 0 0 13_32907420_._GA_G,AA 0 0 0 0 0 0 0 13_32911073_._CA_C,TA 0 0 0 0 0 0 0 13_32911873_._T_A,C 0 0 0 0 0 0 0 13_32912175_._A_G,C 0 0 0 0 0 0 0 13_32912345_._GA_G,AA 0 0 0 0 0 0 0 13_32912472_._C_T,A 0 0 0 0 0 0 0 13_32912674_._A_G,T 0 0 0 0 0 0 0 13_32913558_._CA_C,TA 0 0 0 0 0 0 0 Basically I want to compare my cells to other studies Thanks a lot for comments From: Nico B. ***@***.***> Sent: Monday, May 22, 2023 1:51 AM To: cbg-ethz/BnpC ***@***.***> Cc: Chen, Xianfeng, Ph.D. ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [cbg-ethz/BnpC] how can I map my cells to an previously generated cluster? (Issue #27) Hey, Currently, there is only the argument --fixed_assignment <ASSIGNMENT FILE> implemented, which does not update cluster assignments, but that is not what you want, is it? As I understand (I did not get your example fully), you want to have the assignment flexible/learned but the clusters fixed? You could do the same as for the assignment, init the clusters from a given file, and then just update the assignments and skip the rest of the update steps (https://github.com/cbg-ethz/BnpC/blob/b4dfefc1962b4802ab685604d321548035456e6e/libs/MCMC.py#LL321C27-L321C27). Unfortunately, I don't have the time atm to implement it myself, but let me know if you get stuck somewhere. Cheers - Reply to this email directly, view it on GitHub<#27 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJLCGDO2BY5PAGLMPTEVBADXHMSILANCNFSM6AAAAAAYATPDKA>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>