one_spot_df: one_spot_df

In AbSim: Time Resolved Simulations of Antibody Repertoires

Description

WRC hotspot mutations taken from Yaari et al., Frontiers in Immunology, 2013. These include only the mutations following the WRC pattern, where W equals A or T and R equals A or G). 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.

Usage

one_spot_df

Format

A data frame with 32 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

Source

Yaari et al., Frontiers in Immunology, 2013

AbSim documentation built on May 2, 2019, 5:08 a.m.