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.


datasets

Simulation methods for the evolution of antibody repertoires. The heavy chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins with an initial VDJ recombination event, starting the first phylogenetic tree. Upon completion, the main loop of the algorithm begins, with each iteration representing one simulated time step. Various mutation events are possible at each time step, contributing to a diverse final repertoire.

Alexander Yermanos

AbSim

Time Resolved Simulations of Antibody Repertoires

hotspot_df function

An object of class <code>data.frame</code> with 1024 rows and 6 columns.

Format

Yaari et al., Frontiers in Immunology, 2013

hotspot_df: hotspot_df

Description

Usage

Arguments

Format

Source

Details