getAllSeqs: Return all tip and internal node sequences
In dowser: B Cell Receptor Phylogenetics Toolkit

View source: R/TreeFunctions.R

getAllSeqs

R Documentation

Return all tip and internal node sequences

Description

getNodeSeq Sequence retrieval function.

Usage

getAllSeqs(data, imgt_gaps = TRUE)

Arguments

`data`	a tibble of `airrClone` objects with reconstructed trees, the output of getTrees
`imgt_gaps`	include a column of gapped sequences?

Details

Column names: clone_id = clone id node_id = name of node, either the sequence name if a tip or Node<number> if internal node node = node number in tree. Tips are nodes 1:<number of tips>. locus = locus of sequence sequence = ungapped sequence, either observed for tips or reconstructed for internal nodes sequence_alignment = sequence with IMGT gaps (optional)

Value

A tibble with sequence information for each tip and internal node of a set of trees.

See Also

getTrees getNodeSeq

dowser documentation built on Nov. 5, 2025, 6:36 p.m.

dowser index

Package overview README.md Building trees with paired heavy and light chain data Build Lineage Trees Build Time Trees Using TyCHE and BEAST Discrete Trait Analysis Measurable evolution Plotting Lineage Trees Quickstart Reconstruct Clonal Germlines Reconstruct Intermediate Sequences Build B cell lineage trees Building trees with paired heavy and light chain data Build Time Trees Using TyCHE and BEAST Detect ongoing B cell evolution Discrete trait analysis Dowser: Simple lineage tree construction Plot B cell lineage trees Reconstruct clonal germline sequences Reconstruct intermediate sequences Using data from non-B cells

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

Tweet to @rdrrHQ

GitHub issue tracker

ian@mutexlabs.com