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Alakazam

Alakazam is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides a set of tools to investigate lymphocyte receptor clonal lineages, diversity, gene usage, and other repertoire level properties, with a focus on high-throughput immunoglobulin (Ig) sequencing.

Alakazam serves five main purposes:

  1. Providing core functionality for other R packages in the Immcantation framework. This includes common tasks such as file I/O, basic DNA sequence manipulation, and interacting with V(D)J segment and gene annotations.
  2. Providing an R interface for interacting with the output of the pRESTO and Change-O tool suites.
  3. Performing clonal abundance and diversity analysis on lymphocyte repertoires.
  4. Performing lineage reconstruction on clonal populations of Ig sequences and analyzing the topology of the resultant lineage trees.
  5. Performing physicochemical property analyses of lymphocyte receptor sequences.

Contact

For help and questions please contact the Immcantation Group or use the issue tracker.

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Version

Install

install.packages('alakazam')

Monthly Downloads

1,173

Version

1.1.0

License

AGPL-3

Maintainer

Jason Vander Heiden

Last Published

February 7th, 2021

Functions in alakazam (1.1.0)

DiversityCurve-class

S4 class defining a diversity curve
ABBREV_AA

Amino acid abbreviation translations
ChangeoClone-class

S4 class defining a clone
EdgeTest-class

S4 class defining edge significance
AbundanceCurve-class

S4 class defining a clonal abundance curve
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.
ExampleTrees

Example Ig lineage trees
DEFAULT_COLORS

Default colors
ExampleDbChangeo

Example Change-O database
ExampleDb

Example AIRR database
buildPhylipLineage

Infer an Ig lineage using PHYLIP
baseTheme

Standard ggplot settings
aminoAcidProperties

Calculates amino acid chemical properties for sequence data
countGenes

Tabulates V(D)J allele, gene or family usage.
countClones

Tabulates clones sizes
MRCATest-class

S4 class defining edge significance
calcCoverage

Calculate sample coverage
calcDiversity

Calculate the diversity index
alakazam

The alakazam package
bulk

Calculates the average bulkiness of amino acid sequences
IMGT_REGIONS

IMGT V-segment regions
countPatterns

Count sequence patterns
charge

Calculates the net charge of amino acid sequences.
IUPAC_CODES

IUPAC ambiguous characters
checkColumns

Check data.frame for valid columns and issue message if invalid
nonsquareDist

Calculate pairwise distances between sequences
padSeqEnds

Pads ragged ends of aligned DNA sequences
getSegment

Get Ig segment allele, gene and family names
getPositionQuality

Get a data.frame with sequencing qualities per position
estimateAbundance

Estimates the complete clonal relative abundance distribution
extractVRegion

Extracts FWRs and CDRs from IMGT-gapped sequences
isValidAASeq

Validate amino acid sequences
permuteLabels

Permute the node labels of a tree
summarizeSubtrees

Generate subtree summary statistics for a tree
phyloToGraph

Convert a tree in ape phylo format to igraph graph format.
makeChangeoClone

Generate a ChangeoClone object for lineage construction
getAAMatrix

Build an AA distance matrix
cpuCount

Available CPU cores
aliphatic

Calculates the aliphatic index of amino acid sequences
alphaDiversity

Calculate clonal alpha diversity
collapseDuplicates

Remove duplicate DNA sequences and combine annotations
tableEdges

Tabulate the number of edges between annotations within a lineage tree
gridPlot

Plot multiple ggplot objects
getDNAMatrix

Build a DNA distance matrix
plotMRCATest

Plot the results of a founder permutation test
combineIgphyml

Combine IgPhyML object parameters into a dataframe
plotSubtrees

Plots subtree statistics for multiple trees
plotEdgeTest

Plot the results of an edge permutation test
plotDiversityTest

Plot the results of diversity testing
readChangeoDb

Read a Change-O tab-delimited database file
rarefyDiversity

Generate a clonal diversity index curve
sortGenes

Sort V(D)J genes
stoufferMeta

Weighted meta-analysis of p-values via Stouffer's method
groupGenes

Group sequences by gene assignment
graphToPhylo

Convert a tree in igraph graph format to ape phylo format.
getMRCA

Retrieve the first non-root node of a lineage tree
makeTempDir

Create a temporary folder
getPathLengths

Calculate path lengths from the tree root
maskPositionsByQuality

Mask sequence positions with low quality
pairwiseDist

Calculate pairwise distances between sequences
testEdges

Tests for parent-child annotation enchrichment in lineage trees
testDiversity

Pairwise test of the diversity index
gravy

Calculates the hydrophobicity of amino acid sequences
pairwiseEqual

Calculate pairwise equivalence between sequences
seqDist

Calculate distance between two sequences
maskSeqEnds

Masks ragged leading and trailing edges of aligned DNA sequences
plotAbundanceCurve

Plots a clonal abundance distribution
readFastqDb

Load sequencing quality scores from a FASTQ file
maskSeqGaps

Masks gap characters in DNA sequences
seqEqual

Test DNA sequences for equality.
polar

Calculates the average polarity of amino acid sequences
progressBar

Standard progress bar
plotDiversityCurve

Plot the results of alphaDiversity
testMRCA

Tests for MRCA annotation enrichment in lineage trees
translateDNA

Translate nucleotide sequences to amino acids
readIgphyml

Read in output from IgPhyML
translateStrings

Translate a vector of strings
writeChangeoDb

Write a Change-O tab-delimited database file