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.
1 2 3 4 5 6 7 8 | 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 |
.method |
Either "hamm" (for hamming distance) or "lev" (for edit distance). Passed to the |
.max.errors |
Passed to the |
.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
1 2 3 4 5 6 7 8 | ## 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)
|
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