mutation.network: Make mutation network for the given repertoire.
In tcR: Advanced Data Analysis of Immune Receptor Repertoires

Description Usage Arguments Value See Also Examples

Mutation network (or a mutation graph) is a graph with vertices representing nucleotide or in-frame amino acid sequences (out-of-frame amino acid sequences will automatically filtered out) and edges are connecting pairs of sequences with hamming distance or edit distance between them no more than specified in the .max.errors function parameter.

mutation.network(
  .data,
  .method = c("hamm", "lev"),
  .max.errors = 1,
  .label.col = "CDR3.amino.acid.sequence",
  .seg.col = "V.gene",
  .prob.col = "Probability"
)

`.data`	Either character vector of sequences, data frame with `.label.col` or shared repertoire (result from the `shared.repertoire` function) constructed based on `.label.col`.
`.method`	Either "hamm" (for hamming distance) or "lev" (for edit distance). Passed to the `find.similar.sequences` function.
`.max.errors`	Passed to the `find.similar.sequences` function.
`.label.col`	Name of the column with CDR3 sequences (vertex labels).
`.seg.col`	Name of the column with V gene segments.
`.prob.col`	Name of the column with clonotype probability.

Mutation network, i.e. igraph object with input sequences as vertices labels, ???

shared.repertoire, find.similar.sequences, set.people.vector, get.people.names

## Not run: 
data(twb)
twb.shared <- shared.repertoire(twb)
G <- mutation.network(twb.shared)
get.people.names(G, 300, T)  # "Subj.A|Subj.B"
get.people.names(G, 300, F)  # list(c("Subj.A", "Subj.B"))

## End(Not run)

Loading required package: ggplot2
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Attaching package: ‘dplyr’

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Loading required package: reshape2
Loading required package: igraph

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sh: 1: wc: Permission denied
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========================================
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! The tcR package WILL SOON BE ORPHANED 
!! AND REMOVED FROM CRAN.
!!
!! A new package is available that is 
!! designed to replace tcR: 
!! immunarch  --  https://immunarch.com/
!!
!! We will be happy to help you to move
!! to the new package. Feel free to contact us:
!! http://github.com/immunomind/immunarch
!!
!! Sincerely, 
!!  immunarch dev team and 
!!  Vadim I. Nazarov, lead developer of tcR
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
=======================================

Attaching package: ‘tcR’

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Aggregating sequences...

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[1] "Subj.A|Subj.B"
[[1]]
[1] "Subj.A" "Subj.B"