Calculate clonal frequencies

[Giancarlo mazzetti]

Hi There,

Thank you very much for the bioinformatic pipeline. we all are very grateful for your work.

I have a small question, in my group we work also with clonal frequencies to detect high expanded clones in the B cell repertoire.

Is there any way to calculate the clonal frequencies after the change-o step ? What I would like is to have a new column beside the detected CDR3 with the frequencies that it is present inside the total repertoire (example 0.001, 0.01, 0,05 ecc…).

Thank you in advance for your support.

[Jason Vander Heiden]

Greetings @Giancarlo mazzetti,

This can be done with alakazam::countClones. If you want to expand the results out to the full input data, you can do a left join to duplicate the abundance values across all members of a clone. For example:

library(alakazam)
library(dplyr)
clones <- countClones(ExampleDb, groups="sample_id")
db <- left_join(ExampleDb, clones, by=c("sample_id", "clone_id"))

This will add the same value for sequence_count (number of sequences) and seq_freq (faction of sequences within groups) to each row of the input data with the sample sample_id and clone_id pair.

Alternatively, if you have already subset the data to one row per clone, then you can just sort+cbind or do a standard inner join.

More complicated statistical approaches are here:

https://alakazam.readthedocs.io/en/stable/vignettes/Diversity-Vignette/

[ssnn]

This issue is not active and seems resolved. Reopen if needed.