B Cell Receptor Phylogenetics Toolkit

Documentation for package ‘dowser’ version 2.5.1

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A B C D E F G I M P R S T W

-- A --

airrClone	S4 class defining a clone in Dowser
airrClone-class	S4 class defining a clone in Dowser

-- B --

BiopsyTrees	Example Ig lineage trees with biopsy reconstructions.
bootstrapTrees	Deprecated! Please use findSwitches instead.
buildAllClonalGermlines	buildAllClonalGermlines Determines and builds all possible germlines for a clone
buildBeast	Read in a directory from a BEAST run. Runs treeannotator and loganalyser.
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

-- C --

calcRF	Finds the Robinson-Fould's cluster distance between phylogenies.
checkDivergence	Compare divergence along a tree in terms of mutations (sum of branches) for each tip and reconstructed internal node to its Hamming distance from the germline. Divergence should never be less than Hamming distance. A threshold of -1 is used to represent 1 full mutation difference. The function will throw a warning if any trees cross this threshold
checkNodeDivergences	For each node in nodes list, check that the current divergence is the same as previously reported
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.
createAllGermlines	createAllGermlines Creates all possible germlines for a clone
createGermlines	createGermlines Determine consensus clone sequence and create germline for clone
create_alignment	Takes an airr clone object and returns BEAST2 Alignment xml of the sequences
create_height_prior	Takes an airr clone object and returns BEAST2 XML to set a height prior
create_max_height_prior	Takes an airr clone object and returns BEAST2 XML to set a maximum height prior
create_MRCA_prior_germline	Takes an airr clone object and returns BEAST2 XML for MRCA prior of the germline sequence
create_MRCA_prior_observed	Takes an airr clone object and returns BEAST2 XML for MRCA prior of the observed sequences
create_root_freqs	Takes an airr clone object and returns BEAST2 rootfreqs xml of the germline
create_starting_tree	Takes an airr clone object and tree and returns BEAST2 XML for setting the starting tree
create_traitset	Takes an airr clone object and returns BEAST2 XML for a trait/traitSet from a column

-- D --

dfToFasta	Write a fasta file of sequences 'readFasta' reads a fasta file
downsampleClone	'downsampleClone' Down-sample clone to maximum tip/switch ratio
dowser	The dowser package
dowserObjectEquivalent	'dowserObjectEquivalent' Experimental. Check if two Dowser objects are equivalent

-- E --

ExampleAirr	Example AIRR database
ExampleAirrTyCHE	Example AIRR database for TyCHE
ExampleClones	Example Ig lineage trees
ExampleDbChangeo	Example Change-O database
ExampleMixedClones	Example Multiple Partition Trees
ExampleMixedDb	Example Change-O database
exportTrees	Exports the phylogenetic trees from the airrClone object

-- F --

filterCombs	'filterCombs' Remove sequences likely resulting from oversequencing and PCR error This removes "comb" structures in trees which are flat polytomies with low duplicate counts radiating out from a single node with a much higher duplicate count. Adapted from https://bitbucket.org/kleinstein/projects/src/master/Hoehn2022/isotype_analysis/treesAndSwitches_dowser.R
filterPartialSeqs	'filterPartialSeqs'
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

-- G --

getAllSeqs	Return all tip and internal node sequences
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.
getDiffPoint	Recurse up to tree to find most recent node with different state, or the root
getDiffPoints	For each tree, recurse up to tree to find most recent node with a different state, or the root
getDivergence	Get divergence from root of tree for each tip
getGermline	getGermline get germline segment from specified receptor and segment
getHeightsAndLengths	Add height and length columns to a tree@data data frame
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
getSeqPath	Return all sequences along the tree from the germline to a specified node
getSkylines	Make data frames for Bayesian skyline plots
getSubclones	#' Deprecated! Use resolveLightChains
getSubTaxa	Get the tip labels as part of a clade defined by an internal node
getTimeTrees	Estimate time trees by running BEAST on each clone Applies XML 'template' to each clone
getTimeTreesIterate	Iteratively resume getTimeTrees until convergence, as defined by all parameters (except those in 'ignore' vector) having ESS greater than or equal to the specified ess_cutoff
getTrees	Estimate lineage tree topologies, branch lengths, and internal node states if desired
getTreesAndUCAs	getTreesAndUCAs Construct trees and infer the UCA

-- I --

installPythonDependencies	installPythonDependencies Checks for and installs the Python dependencies for UCA estimation
IsotypeTrees	Example Ig lineage trees with isotype reconstructions.

-- M --

makeAirrClone	Generate a airrClone object for lineage construction
makeModelFile	Make a parsimony model file
makeSkyline	get values for Bayesian Skyline plot
mapSubtrees	Get a map of nodes from one
maskCodons	'maskCodons' Masks codons split by insertions
maskSequences	'maskSequences' Mask codons split by insertions in V gene

-- P --

plotMSA	Simple function for plotting multiple sequence alignments input can be either nucleotide or AA and contain ambiguous characters
plotSkylines	Simple function for plotting Bayesian skyline plots
plotTrees	Plot a tree with colored internal node labels using ggtree

-- R --

readBEAST	Reads in a BEAST output directory
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
readTreesJSON	'readTreesJSON' Experimental. Read trees from JSON/AIRR format from Dowser
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

-- S --

sampleCloneMultiGroup	'sampleCloneMultiGroup' Down-sample clone to specified size with one or multiple groups to sample evenly
sampleClones	'sampleClones' Down-sample clones to specified size
scaleBranches	Scale branch lengths to represent either mutations or mutations per site.
setNodeDivergences	For each node in nodes list, store the divergence from the UCA
stitchRegions	stitchRegions Similar to stitchVDJ but with segment IDs instead of nucleotides
stitchVDJ	stitchVDJ combines germline gene segments to a single string
stopCodonCheck	Check whether sequences have in-frame premature stop codons (PTCs)

-- T --

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.
treesEquivalent	Check whether two tree objects are equivalent
treesToPDF	Simple function for plotting a lot of trees into a pdf

-- W --

writeCloneSequences	Write the sequences used in tree building to a fasta format. If there are more than one tree in airrClone output the sequence id will be followed by "\|clone_id".
writeFasta	'writeFasta' Write a fasta file of sequences given a named list of sequences
writeLineageFile	Write lineage file for IgPhyML use
writeTreesJSON	'writeTreesJSON' Experimental. Write trees in AIRR format
write_clones_to_xmls	Wrapper to write multiple clones to XML files
write_clone_to_xml	Takes an airr clone object and template and writes a BEAST2 XML file