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how can I map my cells to an previously generated cluster? #27
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Hey, Currently, there is only the argument As I understand (I did not get your example fully), you want to have the assignment flexible/learned but the clusters fixed? Unfortunately, I don't have the time atm to implement it myself, but let me know if you get stuck somewhere. Cheers |
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: ***@***.******@***.***>>
|
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: ***@***.******@***.***>>
|
Hi
there is a publication that has their generated cluster by BnpC, and each cluster associates with a function, now how can I map my data to such an existing cluster? (I don't want to use my data to generate any new cluster because I want to map my data to their functions).
this is equivalent to the situation below:
I have 11 samples, and I want to use 10 of them to generate a cluster, and use the 11th sample to map to the pre-generated cluster from the 10 samples.
if current version of BnpC does not support such a request, could you let me know which part of your code needs to be changed?
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