Immunoglobulin Clonal Lineage and Diversity Analysis

Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) , Stern, Yaari and Vander Heiden, et al (2014) .


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 lineage reconstruction on clonal populations of Ig sequences and analyzing the topology of the resultant lineage trees.
  4. Performing clonal abundance and diversity analysis on lymphocyte repertoires.
  5. Performing physicochemical property analyses of lymphocyte receptor sequences.

Contact

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

News

Version 0.2.11: September 12, 2018

General:

  • Added nonsquareDist function to calculate the non-square distance matrix of sequences.
  • Exported some internal utility functions to make them available to dependent packages: progressBar, baseTheme, checkColumns and cpuCount.

Diversity:

  • estimateAbundance, and plotAbundanceCurve, will now allow group=NULL to be specified to performance abundance calculations on ungrouped data.

Gene Usage:

  • Added fill argument to countGenes. When set TRUE this adds zeroes to the group pairs that do not exist in the data.
  • Added new function groupGenes to group sequences sharing same V and J gene.

Toplogy Analysis:

  • Fixed a bug in tableEdges causing it to fail when no parent/child relationships exist when specifying indirect=TRUE.
  • makeChangeoClone will now issue an error and terminate, instead of continuing with a warning, when all sequences are not the same length.

Version 0.2.10: March 30, 2018

General:

  • Fixed a bug in IPUAC_AA wherein X was not properly matching against Q.
  • Changed behavior in getAAMatrix to treat * (stop codon) as a mismatch.

Version 0.2.9: March 21, 2018

General:

  • Added explicit type casting for known columns to readChangeoDb.
  • Added the padSeqEnds function which pads sequences with Ns to make then equal in length.
  • Added verification of unique sequence IDs to collapseDuplicates.

Diversity:

  • Added the uniform argument to rarefyDiversity allowing users to toggle uniform vs non-uniform sampling.
  • Renamed plotAbundance to plotAbundanceCurve.
  • Changed estimateAbundance return object from a data.frame to a new AbundanceCurve custom class.
  • Set default plot call for AbundanceCurve to plotAbundanceCurve.
  • Added the annotate argument from plotDiversityCurve to plotAbundanceCurve.
  • Added the score argument to plotDiversityCurve to toggle between plotting diversity or evenness.
  • Added the function plotDiversityTest to generate a simple plot of DiversityTest object summaries.

Gene Usage:

  • Added the omit_nl argument to getAllele, getGene and getFamily to allow optional filtering of non-localized (NL) genes.

Lineage:

  • Fixed a bug in makeChangeoClone preventing it from interpreting the id argument correctly.
  • Added the pad_end argument to makeChangeoClone to allow automatic padding of ends to make sequences the same length.

Version 0.2.8: September 21, 2017

General:

  • Updated Rcpp dependency to 0.12.12.
  • Added dry argument to collapseDuplicates which will annotate duplicate sequences but not remove them when set to TRUE.
  • Fixed a bug where collapseDuplicates was returning one sequence if all sequences were considered ambiguous.

Lineage:

  • Added ability to change masking character and distance matrix used in makeChangeoClone and buildPhylipLineage for purposes of (optionally) treating indels as mismatches.
  • Fixed a bug in buildPhylipLineage when PHYLIP doesn't generate inferred sequences and has only one block.

Version 0.2.7: June 12, 2017

General:

  • Fixed a bug in readChangeoDb causing the select argument to do nothing.
  • Added progress package dependency.
  • Internal changes to support Rcpp 0.12.11.

Gene Usage:

  • Renamed the count/frequency columns output by countGenes when the clone argument is specified to CLONE_COUNT/CLONE_FREQ.
  • Added a vignette describing basic gene usage analysis.

Version 0.2.6: March 21, 2017

General:

  • License changed to Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0).
  • Removed data.table dependency and added readr dependency.
  • Performance improvements in readChangeoDb and writeChangeoDb.

Version 0.2.5: August 5, 2016

General:

  • Fixed a bug in seqDist() wherein distance was not properly calculated in some sequences containing gap characters.
  • Added stop and gap characters to getAAMatrix() return matrix.

Version 0.2.4: July 20, 2016

General:

  • Added Rcpp and data.table dependencies.
  • Modified readChangeoDb() to wrap data.table::fread() instead of utils::read.table() if the input file is not compressed.
  • Ported testSeqEqual(), getSeqDistance() and getSeqMatrix() to C++ to improve performance of collapseDuplicates() and other dependent functions.
  • Renamed testSeqEqual(), getSeqDistance() and getSeqMatrix() to seqEqual(), seqDist() and pairwiseDist(), respectively.
  • Added pairwiseEqual() which creates a logical sequence distance matrix; TRUE if sequences are identical, FALSE if not, excluding Ns and gaps.
  • Added translation of ambiguous and gap characters to X in translateDNA().
  • Fixed bug in collapseDuplicates() wherein the input data type sanity check would cause the vignette to fail to build under R 3.3.
  • Replaced the ExampleDb.gz file with a larger, more clonal, ExampleDb data object.
  • Replaced ExampleTrees with a larger set of trees.
  • Renamed multiggplot() to gridPlot().

Amino Acid Analysis:

  • Set default to normalize=FALSE for charge calculations to be more consistent with previously published repertoire sequencing results.

Diversity Analysis:

  • Added a progress argument to rarefyDiversity() and testDiversity() to enable the (previously default) progress bar.
  • Fixed a bug in estimateAbundance() were the function would fail if there was only a single input sequence per group.
  • Changed column names in data and summary slots of DiversityTest to uppercase for consistency with other tools.
  • Added dispatching of plot to plotDiversityCurve for DiversityCurve objects.

Gene Usage:

  • Added sortGenes() function to sort V(D)J genes by name or locus position.
  • Added clone argument to countGenes() to allow restriction of gene abundance to one gene per clone.

Topology Analysis:

  • Added a set of functions for lineage tree topology analysis.
  • Added a vignette showing basic tree topology analysis.

Version 0.2.3: February 22, 2016

General:

  • Fixed a bug wherein the package would not build on R < 3.2.0 due to changes in base::nchar().
  • Changed R dependency to R >= 3.1.2.

Version 0.2.2: January 29, 2016

General:

  • Updated license from CC BY-NC-SA 3.0 to CC BY-NC-SA 4.0.
  • Internal changes to conform to CRAN policies.

Amino Acid Analysis:

  • Fixed bug where arguments for the aliphatic() function were not being passed through the ellipsis argument of aminoAcidProperties().
  • Improved amino acid analysis vignette.
  • Added check for correctness of amino acids sequences to aminoAcidProperties().
  • Renamed AA_TRANS to ABBREV_AA.

Diversity:

  • Added evenness and bootstrap standard deviation to rarefyDiversity() output.

Lineage:

  • Added ExampleTrees data with example output from buildPhylipLineage().

Version 0.2.1: December 18, 2015

General:

  • Removed plyr dependency.
  • Added dplyr, lazyeval and stringi dependencies.
  • Added strict requirement for igraph version >= 1.0.0.
  • Renamed getDNADistMatrix() and getAADistMatrix() to getDNAMatrix and getAAMatrix(), respectively.
  • Added getSeqMatrix() which calculates a pairwise distance matrix for a set of sequences.
  • Modified default plot sizing to be more appropriate for export to PDF figures with 7-8 inch width.
  • Added multiggplot() function for performing multiple panel plots.

Amino Acid Analysis:

  • Migrated amino acid property analysis from Change-O CTL to alakazam. Includes the new functions gravy(), bulk(), aliphatic(), polar(), charge(), countPatterns() and aminoAcidProperties().

Annotation:

  • Added support for unusual TCR gene names, such as 'TRGVA*01'.
  • Added removal of 'D' label (gene duplication) from gene names when parsed with getSegment(), getAllele(), getGene() and getFamily(). May be disabled by providing the argument strip_d=FALSE.
  • Added countGenes() to tabulate V(D)J allele, gene and family usage.

Diversity:

  • Added several functions related to analysis of clone size distributions, including countClones(), estimateAbundance() and plotAbundance().
  • Renamed resampleDiversity() to rarefyDiversity() and changed many of the internals. Bootstrapping is now performed on an inferred complete relative abundance distribution.
  • Added support for inclusion of copy number in clone size determination within rarefyDiversity() and testDiversity().
  • Diversity scores and confiderence intervals within rarefyDiversity() and testDiversity() are now calculated using the mean and standard deviation of the bootstrap realizations, rather than the median and upper/lower quantiles.
  • Added ability to add counts to the legend in plotDiversityCurve().

Version 0.2.0: June 15, 2015

Initial public release.

General:

  • Added citations for the citation("alakazam") command.

Version 0.2.0.beta-2015-05-30: May 30, 2015

Lineage:

  • Added more error checking to buildPhylipLineage().

Version 0.2.0.beta-2015-05-26: May 26, 2015

Lineage:

  • Fixed issue where buildPhylipLineage() would hang on R 3.2 due to R change request PR#15508.

Version 0.2.0.beta-2015-05-05: May 05, 2015

Prerelease for review.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("alakazam")

0.2.11 by Jason Vander Heiden, 7 months ago


http://alakazam.readthedocs.org


Report a bug at https://bitbucket.org/kleinstein/alakazam/issues


Browse source code at https://github.com/cran/alakazam


Authors: Jason Vander Heiden [aut, cre] , Namita Gupta [aut] , Susanna Marquez [ctb] , Daniel Gadala-Maria [ctb] , Ruoyi Jiang [ctb] , Nima Nouri [ctb] , Steven Kleinstein [aut, cph]


Documentation:   PDF Manual  


CC BY-SA 4.0 license


Imports dplyr, graphics, grid, igraph, lazyeval, methods, progress, Rcpp, readr, scales, seqinr, stats, stringi, tidyr, utils

Depends on ggplot2

Suggests knitr, rmarkdown, testthat

Linking to Rcpp

System requirements: C++11


Imported by rabhit, scoper, shazam, tigger.


See at CRAN