hotspot_df 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.

@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

data("hotspot_df")

Format

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

Source

Yaari et al., Frontiers in Immunology, 2013