clonalExpansion: Clonally expands the simulated repertoire generated from...

In AbSim: Time Resolved Simulations of Antibody Repertoires

Description

Clonally expands the simulated repertoire generated from fullRepertoire function.

Usage

clonalExpansion(ab.repertoire, rep.size, distribution, with.germline,
  dist.parameters)

Arguments

ab.repertoire	The output from the fullRepertoire function. This takes should be a nested list, with the first element containing a list of sequence arrays, the second element containing the corresponding list of names, and the third element containing a list of trees. The following list elements (containing the sampling information) will be disregarded for repertoire expansion.
rep.size	Controls the total size of the final repertoire. This number should be greater than the total number of sequences that are provided as input. Note that currently using the "powerlaw" distribution will return less than the exact rep.size parameter due to integer values of clonal frequencies.
distribution	This parameter controls how the clonal frequency of the repertoire is distributed. Options include "powerlaw" ("pl"), "identical" ("id")
with.germline	Logical - If false, the germline from each lineage will be removed.
dist.parameters	Supplies the parameters for how the clonal frequencies should be distributed.

Value

Returns a list with three elements. The first list element contains a character array, with the sequences composing the repertoire. The second element is a character array with the names of the sequences, and the third element in the list corresponds to the original phylogenetic trees that served as the basis for expansion

See Also

fullRepertoire

Examples

## Not run: 
clonalExpansion(ab.repertoire=fullRepertoire.output,
 rep.size=3*length(unlist(fullRepertoire.output[[1]])),
 distribution="identical",
 with.germline="FALSE")

## End(Not run)

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