alakazam (version 0.2.2)

alakazam: The alakazam package

Description

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

• Providing core functionality for other R packages in the Change-O suite. This includes common tasks such as file I/O and basic DNA sequence manipulation.
• Providing an R interface for interacting with the output of the pRESTO tool suite.
• Providing tools to perform lineage reconstruction and diversity analysis on clonal populations of immunoglobulin (Ig) 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.

Diversity analysis

• countClones: Calculate clonal abundance.
• estimateAbundance: Infer complete clonal abundance distribution with confidence intervals.
• rarefyDiversity: Generate clonal diversity curves.
• testDiversity: Test significance of clonal diversity scores.
• plotAbundance: Plot clone size distribution as a rank-abundance curve.
• plotDiversityCurve: Plot clonal diversity curves.

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

• getSeqDistance: Calculate Hamming distance between sequences.
• getSeqMatrix: Calculate a matrix of pairwise Hamming distances for a sequence set.
• testSeqEqual: Test sequences for equality.

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. Under review.