MMR in SHmulate

ssnn

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The same question was sent to and answered from immcantation@googlegroups.com Reopen if needed.

The Shmulate function simulates mutations under the S5F model, which is an empirical model of somatic hypermutation targeting and substitution. This paper details how the S5F model was developed: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828525/. Because it is an empirical model, it doesn't explicitly model the different molecular pathways that produce mutations in SHM. Instead, it describes the relative mutation rates and substitution probabilities of all nucleotide 5-mers inferred from the empirical data in the paper. Shmulate uses these mutation and substitution probabilities to introduce point mutations into sequences.

2021-10-14T11:47:32+00:00

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ssnn
- changed status to resolved
The same question was sent to and answered from immcantation@googlegroups.com Reopen if needed.

The Shmulate function simulates mutations under the S5F model, which is an empirical model of somatic hypermutation targeting and substitution. This paper details how the S5F model was developed: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828525/. Because it is an empirical model, it doesn't explicitly model the different molecular pathways that produce mutations in SHM. Instead, it describes the relative mutation rates and substitution probabilities of all nucleotide 5-mers inferred from the empirical data in the paper. Shmulate uses these mutation and substitution probabilities to introduce point mutations into sequences.
- 2021-10-14T11:47:32+00:00
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