Immunoglobulin Clonal Lineage and Diversity Analysis

Documentation for package ‘alakazam’ version 1.3.0

Help Pages

-- 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 --

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 --

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	Plot 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 enrichment 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 --

Write a Change-O tab-delimited database file