hotspot_df: hotspot_df
In AbSim: Time Resolved Simulations of Antibody Repertoires

Description Usage Format Details Source

Hotspot mutations taken from Yaari et al., Frontiers in Immunology, 2013. This contains transition probabilities for all 5mer combinations based on high throughput sequencing data. The transition probabilities are for the middle nucleotide in each 5mer set. This can be customized by changing the genes and sequences. Custom mutation hotspots can be supplied by modifying this dataframe. Repeating particular hotspot entries allows for the hotspot to mutate more than one time per SHM event.

1	hotspot_df

An object of class data.frame with 1024 rows and 6 columns.

@format A data frame with 1024 rows and 6 variables:

pattern: Character array where each entry corresponds to a 5 base motif. The mutation probabilities correspond to the middle nucleotide in each 5mer.
toA: The probability for the middle nucleotide in "pattern" to mutate to an adenine
toC: The probability for the middle nucleotide in "pattern" to mutate to an cytosine
toG: The probability for the middle nucleotide in "pattern" to mutate to an guanine
toT: The probability for the middle nucleotide in "pattern" to mutate to an thymine
Source: The origin of how this motif was discovered. Either Inferred or Experimental