motif_implantation {immuneSIM}

Implant random or predefined motifs into CDR3

Description

Implant random or predefined motifs into CDR3

Usage

motif_implantation(sim_repertoire, motif, fixed_pos = 0)

Arguments

sim_repertoire

An annotated AIRR compliant immuneSIM repertoire.

motif

Either a list that contains number, length and frequencies of motifs or dataframe that contains predefined motifs and their frequencies

fixed_pos

defines position at which motif is to be introduced. if 0 motif will be introduced at random position

Value

Repertoire with modified sequences containing implanted motifs in CDR3.

Examples

sim_repertoire <- list_example_repertoires[["example_repertoire_A"]]
sim_rep_motifs <- motif_implantation(sim_repertoire,list("n"=2,"k"=3,"freq"=c(0.1,0.1)),0)