# Immunoglobulin Clonal Lineage and Diversity Analysis

## Documentation for package ‘alakazam’ version 1.2.0

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

## Help Pages

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

## -- A --

ABBREV_AA | Amino acid abbreviation translations
AbundanceCurve | S4 class defining a clonal abundance curve
AbundanceCurve-class | S4 class defining a clonal abundance curve
AbundanceCurve-method | S4 class defining a clonal abundance curve
alakazam | The alakazam package
aliphatic | Calculates the aliphatic index of amino acid sequences
alphaDiversity | Calculate clonal alpha diversity
aminoAcidProperties | Calculates amino acid chemical properties for sequence data

## -- B --

baseTheme | Standard ggplot settings
buildPhylipLineage | Infer an Ig lineage using PHYLIP
bulk | Calculates the average bulkiness of amino acid sequences

## -- C --

calcCoverage | Calculate sample coverage
calcDiversity | Calculate the diversity index
ChangeoClone | S4 class defining a clone
ChangeoClone-class | S4 class defining a clone
charge | Calculates the net charge of amino acid sequences.
checkColumns | Check data.frame for valid columns and issue message if invalid
collapseDuplicates | Remove duplicate DNA sequences and combine annotations
combineIgphyml | Combine IgPhyML object parameters into a dataframe
countClones | Tabulates clones sizes
countGenes | Tabulates V(D)J allele, gene or family usage.
countPatterns | Count sequence patterns
cpuCount | Available CPU cores

## -- D --

DEFAULT_COLORS | Default colors
DiversityCurve | S4 class defining a diversity curve
DiversityCurve-class | S4 class defining a diversity curve
DiversityCurve-method | S4 class defining a diversity curve
DNA_COLORS | Default colors
DNA_IUPAC | IUPAC ambiguous characters

## -- E --

EdgeTest | S4 class defining edge significance
EdgeTest-class | S4 class defining edge significance
EdgeTest-method | S4 class defining edge significance
estimateAbundance | Estimates the complete clonal relative abundance distribution
Example10x | Small example 10x Genomics Ig V(D)J sequences from CD19+ B cells isolated from PBMCs of a healthy human donor. Down-sampled from data provided by 10x Genomics under a Creative Commons Attribute license, and processed with their Cell Ranger pipeline.
ExampleDb | Example AIRR database
ExampleDbChangeo | Example Change-O database
ExampleTrees | Example Ig lineage trees
extractVRegion | Extracts FWRs and CDRs from IMGT-gapped sequences

## -- G --

getAAMatrix | Build an AA distance matrix
getAllele | Get Ig segment allele, gene and family names
getChain | Get Ig segment allele, gene and family names
getDNAMatrix | Build a DNA distance matrix
getFamily | Get Ig segment allele, gene and family names
getGene | Get Ig segment allele, gene and family names
getLocus | Get Ig segment allele, gene and family names
getMRCA | Retrieve the first non-root node of a lineage tree
getPathLengths | Calculate path lengths from the tree root
getPositionQuality | Get a data.frame with sequencing qualities per position
getSegment | Get Ig segment allele, gene and family names
graphToPhylo | Convert a tree in igraph 'graph' format to ape 'phylo' format.
gravy | Calculates the hydrophobicity of amino acid sequences
gridPlot | Plot multiple ggplot objects
groupGenes | Group sequences by gene assignment

## -- I --

IG_COLORS | Default colors
IMGT_REGIONS | IMGT V-segment regions
isValidAASeq | Validate amino acid sequences
IUPAC_AA | IUPAC ambiguous characters
IUPAC_CODES | IUPAC ambiguous characters
IUPAC_DNA | IUPAC ambiguous characters

## -- J --

junctionAlignment | Calculate junction region alignment properties

## -- M --

makeChangeoClone | Generate a ChangeoClone object for lineage construction
makeTempDir | Create a temporary folder
maskPositionsByQuality | Mask sequence positions with low quality
maskSeqEnds | Masks ragged leading and trailing edges of aligned DNA sequences
maskSeqGaps | Masks gap characters in DNA sequences
MRCATest | S4 class defining edge significance
MRCATest-class | S4 class defining edge significance
MRCATest-method | S4 class defining edge significance

## -- N --

nonsquareDist | Calculate pairwise distances between sequences

## -- P --

padSeqEnds | Pads ragged ends of aligned DNA sequences
pairwiseDist | Calculate pairwise distances between sequences
pairwiseEqual | Calculate pairwise equivalence between sequences
permuteLabels | Permute the node labels of a tree
phyloToGraph | Convert a tree in ape 'phylo' format to igraph 'graph' format.
plot-method | S4 class defining a clonal abundance curve
plot-method | S4 class defining a diversity curve
plot-method | S4 class defining edge significance
plot-method | S4 class defining edge significance
plotAbundanceCurve | Plots a clonal abundance distribution
plotDiversityCurve | Plot the results of alphaDiversity
plotDiversityTest | Plot the results of diversity testing
plotEdgeTest | Plot the results of an edge permutation test
plotMRCATest | Plot the results of a founder permutation test
plotSubtrees | Plots subtree statistics for multiple trees
polar | Calculates the average polarity of amino acid sequences
print-method | S4 class defining a clonal abundance curve
print-method | S4 class defining a diversity curve
print-method | S4 class defining edge significance
print-method | S4 class defining edge significance
progressBar | Standard progress bar

## -- R --

rarefyDiversity | Generate a clonal diversity index curve
readChangeoDb | Read a Change-O tab-delimited database file
readFastqDb | Load sequencing quality scores from a FASTQ file
readIgphyml | Read in output from IgPhyML

## -- S --

seqDist | Calculate distance between two sequences
seqEqual | Test DNA sequences for equality.
SingleDb | Single sequence AIRR database
sortGenes | Sort V(D)J genes
stoufferMeta | Weighted meta-analysis of p-values via Stouffer's method
summarizeSubtrees | Generate subtree summary statistics for a tree

## -- T --

tableEdges | Tabulate the number of edges between annotations within a lineage tree
testDiversity | Pairwise test of the diversity index
testEdges | Tests for parent-child annotation enchrichment in lineage trees
testMRCA | Tests for MRCA annotation enrichment in lineage trees
translateDNA | Translate nucleotide sequences to amino acids
translateStrings | Translate a vector of strings
TR_COLORS | Default colors

## -- W --

writeChangeoDb | Write a Change-O tab-delimited database file