Time Resolved Simulations of Antibody Repertoires


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Documentation for package ‘AbSim’ version 0.2.6

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clonalExpansion Clonally expands the simulated repertoire generated from fullRepertoire function.
fullRepertoire Simulates full heavy chain antibody repertoires for either human or mice.
hotspot_df hotspot_df
ighd_hum_df ighd_hum_df
ighd_mus_df ighd_mus_df
ighj_hum_df ighj_hum_df
ighj_mus_df ighj_mus_df
ighv_hum_df ighv_hum_df
ighv_mus_df ighv_mus_df
igkj_hum_df igkj_hum_df
igkj_mus_df igkj_mus_df
igkv_hum_df igkv_hum_df
igkv_mus_df igkv_mus_df
iglj_hum_df iglj_hum_df
iglj_mus_df iglj_mus_df
iglv_hum_df iglv_hum_df
iglv_mus_df iglv_mus_df
one_spot_df one_spot_df
repertoireFastas Converts AbSim's output sequences and names into fasta file format. Each tree within the repertire will be stored in an individual fasta file. Utilizes sink() and cloneAllConnections() from R base
singleLineage Antibody lineage simulations using only one set of V(D)J germline genes. The main difference between this function and the fullRepertoire function is that there can be multiple VDJ recombination events within one tree. Each VDJ recombination event in the singleLineage function is a branching event within the existing tree, whereas the VDJ recombination events in the fullRepertoire function start a new tree.