getNodeSeq - Return IMGT gapped sequence of specified tree node

Description¶

getNodeSeq Sequence retrieval function.

Usage¶

getNodeSeq(data, node, tree = NULL, clone = NULL, check = TRUE, gaps = TRUE)

Arguments¶

data

a tibble of airrClone objects, the output of getTrees

node

numeric node in tree (see details)

tree

a phylo tree object containing node

clone

if tree not specified, supply clone ID in data

check

check node divergences beforehand (see checkNodeDivergences)

gaps

add IMGT gaps to output sequences?

Value¶

A vector with sequence for each locus at a specified node in tree.

Details¶

Use plotTrees(trees)[[1]] + geom_label(aes(label=node))+geom_tippoint() to show node labels, and getNodeSeq to return internal node sequences

See also¶

getTrees