Immunoglobulin Clonal Lineage and Diversity Analysis


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Documentation for package ‘alakazam’ version 1.1.0

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A B C D E G I 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

-- 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.
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