The alakazam package

Description

alakazam in a member of the Change-O suite of tools and serves five main purposes:

• Providing core functionality for other R packages in the Change-O suite. This includes common tasks such as file I/O, basic DNA sequence manipulation, and interacting with V(D)J segment and gene annotations.

• Providing an R interface for interacting with the output of the pRESTO tool suite.

• Performing lineage reconstruction on clonal populations of immunoglobulin (Ig) sequences.

• Performing clonal abundance and diversity analysis on lymphocyte repertoires.

• Performing physicochemical property analyses of lymphocyte receptor sequences.

For additional details regarding the use of the alakazam package see the vignettes:
browseVignettes("alakazam")

File I/O

• readChangeoDb: Input Change-O style files.

• writeChangeoDb: Output Change-O style files.

Sequence cleaning

• maskSeqEnds: Mask ragged ends.

• maskSeqGaps: Mask gap characters.

• collapseDuplicates: Remove duplicate sequences.

Lineage reconstruction

• makeChangeoClone: Clean sequences for lineage reconstruction.

• buildPhylipLineage: Perform lineage reconstruction of Ig sequences.

Lineage topology analysis

• tableEdges: Tabulate annotation relationships over edges.

• testEdges: Significance testing of annotation edges.

• testMRCA: Significance testing of MRCA annotations.

• summarizeSubtrees: Various summary statistics for subtrees.

• plotSubtrees: Plot distributions of summary statistics for a population of trees.

Diversity analysis

• countClones: Calculate clonal abundance.

• estimateAbundance: Bootstrap clonal abundance curves.

• alphaDiversity: Generate clonal alpha diversity curves.

• plotAbundanceCurve: Plot clone size distribution as a rank-abundance

• plotDiversityCurve: Plot clonal diversity curves.

• plotDiversityTest: Plot testing at given diversity hill indicex.

Ig and TCR sequence annotation

• countGenes: Calculate Ig and TCR allele, gene and family usage.

• extractVRegion: Extract CDRs and FWRs sub-sequences.

• getAllele: Get V(D)J allele names.

• getGene: Get V(D)J gene names.

• getFamily: Get V(D)J family names.

Sequence distance calculation

• seqDist: Calculate Hamming distance between two sequences.

• seqEqual: Test two sequences for equivalence.

• pairwiseDist: Calculate a matrix of pairwise Hamming distances for a set of sequences.

• pairwiseEqual: Calculate a logical matrix of pairwise equivalence for a set of sequences.

Amino acid propertes

• translateDNA: Translate DNA sequences to amino acid sequences.

• aminoAcidProperties: Calculate various physicochemical properties of amino acid sequences.

• countPatterns: Count patterns in sequences.

General data manipulation

• translateStrings: Perform multiple string replacement operations.

References

1. Vander Heiden JA, Yaari G, et al. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014 30(13):1930-2.

2. Stern JNH, Yaari G, Vander Heiden JA, et al. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. 2014 6(248):248ra107.

3. Wu Y-CB, et al. Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis. J Allergy Clin Immunol. 2014 134(3):604-12.

4. Gupta NT, Vander Heiden JA, et al. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics. 2015 Oct 15;31(20):3356-8.