Man pages for dowser
B Cell Receptor Phylogenetics Toolkit
| airrClone-class | S4 class defining a clone in Dowser |
| BiopsyTrees | Example Ig lineage trees with biopsy reconstructions. |
| bootstrapTrees | Deprecated! Please use findSwitches instead. |
| buildAllClonalGermlines | buildAllClonalGermlines Determines and builds all possible... |
| buildBeast | Read in a directory from a BEAST run. Runs treeannotator and... |
| buildClonalGermline | 'buildClonalGermline' Determine consensus clone sequence and... |
| buildGermline | 'buildGermline' reconstruct germline segments from alignment... |
| 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... |
| checkDivergence | Compare divergence along a tree in terms of mutations (sum of... |
| checkNodeDivergences | For each node in nodes list, check that the current... |
| 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... |
| correlationTest | Run date randomization test for temporal signal on a set of... |
| create_alignment | Takes an airr clone object and returns BEAST2 Alignment xml... |
| createAllGermlines | createAllGermlines Creates all possible germlines for a clone |
| createGermlines | createGermlines Determine consensus clone sequence and create... |
| create_height_prior | Takes an airr clone object and returns BEAST2 XML to set a... |
| create_max_height_prior | Takes an airr clone object and returns BEAST2 XML to set a... |
| create_MRCA_prior_germline | Takes an airr clone object and returns BEAST2 XML for MRCA... |
| create_MRCA_prior_observed | Takes an airr clone object and returns BEAST2 XML for MRCA... |
| create_root_freqs | Takes an airr clone object and returns BEAST2 rootfreqs xml... |
| create_starting_tree | Takes an airr clone object and tree and returns BEAST2 XML... |
| create_traitset | Takes an airr clone object and returns BEAST2 XML for a... |
| dfToFasta | Write a fasta file of sequences 'readFasta' reads a fasta... |
| downsampleClone | 'downsampleClone' Down-sample clone to maximum tip/switch... |
| dowser | The dowser package |
| dowserObjectEquivalent | 'dowserObjectEquivalent' Experimental. Check if two Dowser... |
| dowser-package | dowser: B Cell Receptor Phylogenetics Toolkit |
| 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 |
| filterCombs | 'filterCombs' Remove sequences likely resulting from... |
| filterPartialSeqs | 'filterPartialSeqs' |
| findSwitches | Create a bootstrap distribution for clone sequence... |
| formatClones | Generate an ordered list of airrClone objects for lineage... |
| getAllSeqs | Return all tip and internal node sequences |
| getBootstraps | Creates a bootstrap distribution for clone sequence... |
| getDiffPoint | Recurse up to tree to find most recent node with different... |
| getDiffPoints | For each tree, recurse up to tree to find most recent node... |
| getDivergence | Get divergence from root of tree for each tip |
| getGermline | getGermline get germline segment from specified receptor and... |
| 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.... |
| getSeq | Deprecated! Use getNodeSeq |
| getSeqPath | Return all sequences along the tree from the germline to a... |
| 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... |
| getTimeTrees | Estimate time trees by running BEAST on each clone Applies... |
| getTimeTreesIterate | Iteratively resume getTimeTrees until convergence, as defined... |
| getTrees | Estimate lineage tree topologies, branch lengths, and... |
| getTreesAndUCAs | getTreesAndUCAs Construct trees and infer the UCA |
| installPythonDependencies | installPythonDependencies Checks for and installs the Python... |
| 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 |
| 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 |
| plotMSA | Simple function for plotting multiple sequence alignments... |
| 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... |
| 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... |
| reconIgPhyML | Do IgPhyML maximum parsimony reconstruction |
| rerootTree | Reroot phylogenetic tree to have its germline sequence at a... |
| resolveLightChains | Define subgroups within clones based on light chain... |
| resolvePolytomies | Resolve polytomies to have the minimum number of single... |
| runCorrelationTest | Run correlationTest, based on... |
| sampleCloneMultiGroup | 'sampleCloneMultiGroup' Down-sample clone to specified size... |
| sampleClones | 'sampleClones' Down-sample clones to specified size |
| scaleBranches | Scale branch lengths to represent either mutations or... |
| setNodeDivergences | For each node in nodes list, store the divergence from the... |
| stitchRegions | stitchRegions Similar to stitchVDJ but with segment IDs... |
| stitchVDJ | stitchVDJ combines germline gene segments to a single string |
| stopCodonCheck | Check whether sequences have in-frame premature stop codons... |
| 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 |
| writeCloneSequences | Write the sequences used in tree building to a fasta 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... |
| writeFasta | 'writeFasta' Write a fasta file of sequences given a named... |
| writeLineageFile | Write lineage file for IgPhyML use |
| writeTreesJSON | 'writeTreesJSON' Experimental. Write trees in AIRR format |
