General:
IPUAC_AA wherein X was not properly matching against Q.getAAMatrix to treat * (stop codon) as a mismatch.General:
readChangeoDb.padSeqEnds function which pads sequences with Ns to make then equal in length.collapseDuplicates.Diversity:
uniform argument to rarefyDiversity allowing users to toggle uniform vs non-uniform sampling.plotAbundance to plotAbundanceCurve.estimateAbundance return object from a data.frame to a new AbundanceCurve custom class.plot call for AbundanceCurve to plotAbundanceCurve.annotate argument from plotDiversityCurve to plotAbundanceCurve.score argument to plotDiversityCurve to toggle between plotting diversity or evenness.plotDiversityTest to generate a simple plot of DiversityTest object summaries.Gene Usage:
omit_nl argument to getAllele, getGene and getFamily to allow optional filtering of non-localized (NL) genes.Lineage:
makeChangeoClone preventing it from interpreting the id argument correctly.pad_end argument to makeChangeoClone to allow automatic padding of ends to make sequences the same length.General:
dry argument to collapseDuplicates which will annotate duplicate sequences but not remove them when set to TRUE.collapseDuplicates was returning one sequence if all sequences were considered ambiguous.Lineage:
makeChangeoClone and buildPhylipLineage for purposes of (optionally) treating indels as mismatches.buildPhylipLineage when PHYLIP doesn’t generate inferred sequences and has only one block.General:
readChangeoDb causing the select argument to do nothing.Gene Usage:
countGenes when the clone argument is specified to CLONE_COUNT/CLONE_FREQ.General:
readChangeoDb and writeChangeoDb.General:
seqDist() wherein distance was not properly calculated in some sequences containing gap characters.getAAMatrix() return matrix.General:
readChangeoDb() to wrap data.table::fread() instead of utils::read.table() if the input file is not compressed.testSeqEqual(), getSeqDistance() and getSeqMatrix() to C++ to improve performance of collapseDuplicates() and other dependent functions.testSeqEqual(), getSeqDistance() and getSeqMatrix() to seqEqual(), seqDist() and pairwiseDist(), respectively.pairwiseEqual() which creates a logical sequence distance matrix; TRUE if sequences are identical, FALSE if not, excluding Ns and gaps.X in translateDNA().collapseDuplicates() wherein the input data type sanity check would cause the vignette to fail to build under R 3.3.ExampleDb.gz file with a larger, more clonal, ExampleDb data object.ExampleTrees with a larger set of trees.multiggplot() to gridPlot().Amino Acid Analysis:
normalize=FALSE for charge calculations to be more consistent with previously published repertoire sequencing results.Diversity Analysis:
progress argument to rarefyDiversity() and testDiversity() to enable the (previously default) progress bar.estimateAbundance() were the function would fail if there was only a single input sequence per group.data and summary slots of DiversityTest to uppercase for consistency with other tools.plot to plotDiversityCurve for DiversityCurve objects.Gene Usage:
sortGenes() function to sort V(D)J genes by name or locus position.clone argument to countGenes() to allow restriction of gene abundance to one gene per clone.Topology Analysis:
General:
base::nchar().General:
Amino Acid Analysis:
aliphatic() function were not being passed through the ellipsis argument of aminoAcidProperties().aminoAcidProperties().AA_TRANS to ABBREV_AA.Diversity:
rarefyDiversity() output.Lineage:
ExampleTrees data with example output from buildPhylipLineage().General:
getDNADistMatrix() and getAADistMatrix() to getDNAMatrix and getAAMatrix(), respectively.getSeqMatrix() which calculates a pairwise distance matrix for a set of sequences.multiggplot() function for performing multiple panel plots.Amino Acid Analysis:
gravy(), bulk(), aliphatic(), polar(), charge(), countPatterns() and aminoAcidProperties().Annotation:
getSegment(), getAllele(), getGene() and getFamily(). May be disabled by providing the argument strip_d=FALSE.countGenes() to tabulate V(D)J allele, gene and family usage.Diversity:
countClones(), estimateAbundance() and plotAbundance().resampleDiversity() to rarefyDiversity() and changed many of the internals. Bootstrapping is now performed on an inferred complete relative abundance distribution.rarefyDiversity() and testDiversity().rarefyDiversity() and testDiversity() are now calculated using the mean and standard deviation of the bootstrap realizations, rather than the median and upper/lower quantiles.plotDiversityCurve().Initial public release.
General:
citation("alakazam") command.Lineage:
buildPhylipLineage().Lineage:
buildPhylipLineage() would hang on R 3.2 due to R change request PR#15508.Prerelease for review.