View source: R/clonalCluster.R
clonalCluster | R Documentation |
This function uses edit distances of either the nucleotide or amino acid
sequences of the CDR3 and V genes to cluster similar TCR/BCRs together.
As a default, the function takes the input from combineTCR
,
combineBCR
or combineExpression
and amends a
cluster to the data frame or meta data. If exportGraph is set
to TRUE, the function returns an igraph object of the connected sequences.
clonalCluster(
input.data,
chain = "TRB",
sequence = "aa",
samples = NULL,
threshold = 0.85,
group.by = NULL,
exportGraph = FALSE
)
input.data |
The product of |
chain |
Indicate if both or a specific chain should be used - e.g. "both", "TRA", "TRG", "IGH", "IGL". |
sequence |
Clustering based on either "aa" or "nt". |
samples |
The specific samples to isolate for visualization. |
threshold |
The normalized edit distance to consider. The higher the number the more similarity of sequence will be used for clustering. |
group.by |
The column header used for to group contigs. If (NULL), clusters will be calculated across samples. |
exportGraph |
Return an igraph object of connected sequences (TRUE) or the amended input with a new cluster-based variable (FALSE). |
Either amended input with edit-distanced clusters added or igraph object of connect sequences
# Getting the combined contigs
combined <- combineTCR(contig_list,
samples = c("P17B", "P17L", "P18B", "P18L",
"P19B","P19L", "P20B", "P20L"))
sub_combined <- clonalCluster(combined[c(1,2)],
chain = "TRA",
sequence = "aa")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.