| 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. |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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. |
| 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 |
| 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 |
| IsotypeTrees |
Example Ig lineage trees with isotype reconstructions. |
| makeAirrClone |
Generate a airrClone object for lineage construction |
| makeModelFile |
Make a parsimony model file |
| makeSkyline |
get values for Bayesian Skyline plot |
| maskCodons |
'maskCodons' Masks codons split by insertions |
| maskSequences |
'maskSequences' Mask codons split by insertions in V gene |
| plotSkylines |
Simple function for plotting Bayesian skyline plots |
| plotTrees |
Plot a tree with colored internal node labels using ggtree |
| 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 |
| 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 |
| 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. |
| 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) |
| 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 |
| 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". |
| writeLineageFile |
Write lineage file for IgPhyML use |
| 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 |
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)