# B Cell Receptor Phylogenetics Toolkit

## Documentation for package ‘dowser’ version 2.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

airrClone | S4 class defining a clone in Dowser
airrClone-class | S4 class defining a clone in Dowser
BiopsyTrees | Example Ig lineage trees with biopsy reconstructions.
bootstrapTrees | Deprecated! Please use findSwitches instead.
buildClonalGermline | 'buildClonalGermline' Determine consensus clone sequence and create germline for clone
buildGermline | 'buildGermline' reconstruct germline segments from alignment data
buildIgphyml | Wrapper to build IgPhyML trees and infer intermediate nodes
buildPhylo | Wrapper for alakazam::buildPhylipLineage
buildPML | Wrapper for phangorn::optim.pml
buildPratchet | Wrapper for phangorn::pratchet
buildRAxML | Wrapper to build RAxML-ng trees and infer intermediate nodes
calcRF | Finds the Robinson-Fould's cluster distance between phylogenies.
collapseNodes | Collapse internal nodes with the same predicted sequence
colorTrees | Get a color palette for a predefined set of trait values
condenseTrees | Condense a set of equally parsimonious node labels into a single tree
correlationTest | Run date randomization test for temporal signal on a set of trees.
createGermlines | createGermlines Determine consensus clone sequence and create germline for clone
downsampleClone | 'downsampleClone' Down-sample clone to maximum tip/switch ratio
dowser | The dowser package
ExampleAirr | Example AIRR database
ExampleClones | Example Ig lineage trees
ExampleDbChangeo | Example Change-O database
ExampleMixedClones | Example Multiple Partition Trees
ExampleMixedDb | Example Change-O database
findSwitches | Create a bootstrap distribution for clone sequence alignments, and estimate trees for each bootstrap replicate.
formatClones | Generate an ordered list of airrClone objects for lineage construction
getBootstraps | Creates a bootstrap distribution for clone sequence alignments, and returns estimated trees for each bootstrap replicate as a nested list as a new input tibble column.
getDivergence | Get divergence from root of tree for each tip
getGermline | getGermline get germline segment from specified receptor and segment
getNodeSeq | Return IMGT gapped sequence of specified tree node
getPalette | Get a color palette for a predefined set of trait values. 'Germline' defaults to black unless specified.
getSeq | Deprecated! Use getNodeSeq
getSubclones | #' Deprecated! Use resolveLightChains
getSubTaxa | Get the tip labels as part of a clade defined by an internal node
getTrees | Estimate lineage tree topologies, branch lengths, and internal node states if desired
IsotypeTrees | Example Ig lineage trees with isotype reconstructions.
makeAirrClone | Generate a airrClone object for lineage construction
makeModelFile | Make a parsimony model file
maskCodons | 'maskCodons' Masks codons split by insertions
maskSequences | 'maskSequences' Mask codons split by insertions in V gene
plotTrees | Plot a tree with colored internal node labels using ggtree
readFasta | Read a fasta file into a list of sequences 'readFasta' reads a fasta file
readIMGT | 'readIMGT' read in IMGT database
readLineages | Read in all trees from a lineages file
readModelFile | Read in a parsimony model file
reconIgPhyML | Do IgPhyML maximum parsimony reconstruction
rerootTree | Reroot phylogenetic tree to have its germline sequence at a zero-length branch to a node which is the direct ancestor of the tree's UCA. Assigns 'uca' to be the ancestral node to the tree's germline sequence, as 'germid' as the tree's germline sequence ID.
resolveLightChains | Define subgroups within clones based on light chain rearrangements
resolvePolytomies | Resolve polytomies to have the minimum number of single timepoint clades
runCorrelationTest | Run correlationTest, based on https://doi.org/10.1111/2041-210X.12466
scaleBranches | Scale branch lengths to represent either mutations or mutations per site.
stitchRegions | stitchRegions Similar to stitchVDJ but with segment IDs instead of nulecotides
stitchVDJ | stitchVDJ combines germline gene segments to a single string
testPS | Performs PS (parsimony score) test on switch data
testSC | Performs SC (switch count) test on switch data
testSP | Performs SP (switch proportion) test on switch data
TimeTrees | Example Ig lineage trees sampled over time.
treesToPDF | Simple function for plotting a lot of trees into a pdf
writeLineageFile | Write lineage file for IgPhyML use