General:
junctionAlignment, which counts the number of nucleotides in the reference germline not present in the alignment, and the number of V and J nucleotides in the CDR3.Gene Usage:
getFamily where temporary designation gene names were not being correctly subset to the cluster (family) level.Lineage:
runPhylip which was causing buildPhylipLineage to fail when run on Windows.General:
readFastqDb, which reads a repertoire’s .fastq file and imports the sequencing quality scores for sequence_alignment. Added maskPositionsByQuality masks positions that have a sequencing quality score lower than the specified threshold. The convenience function getPositionQuality will create a data.frame with quality scores per position.dplyr dependency to v1.0.padSeqEnds, the argument mod3=TRUE has been added so that sequences are padded to a length that is a multiple of 3.translateDNA where NA values weren’t being translated properly.Amino Acid Analysis:
aminoAcidProperties, which will now default to nt=TRUE.Diversity: + Added a parameter to countClones (remove_na) that will remove all rows with NA values in the clone column if TRUE (default) and issue a warning with how many were removed. If FALSE, those rows will be kept instead.
Gene Usage:
getLocus to extract the locus information from the segment call.getChain to define the chain from the segment or locus call.countGenes to give a warning instead of an error so as not to disrupt running workflows.getSegment where filtering of non-localized genes was not being applied when called from getFamily, because the “NL” part of the name was removed before the filtering step.getAllele, getGene, getFamily and getLocus, to parse constant region gene names correctly.getSegment to be able to parse constant region gene names correctly and not remove the “D” from “IGHD” when strip_d=TRUE.Lineage:
branch_length argument to buildPhylipLineage, and augmented graphToPhylo and phyloToGraph to track intermediate sequence in nodes for phylo object.countGenes (remove_na) that will remove all rows with NA values in the gene column if TRUE (default) and issue a warning with how many were removed. If FALSE, those rows will be kept instead.Diversity:
plotDiversityTest that caused all values of q to appear on the plot rather than just the specified one.Gene Usage:
groupGenes where the v_callj_call column for J gene grouping.groupGenes.only_igh argument of groupGenes to only_heavy.Backwards Incompatible Changes:
V_CALL (Change-O) as the default to identify the field that stored the V gene calls, they now use v_call (AIRR). That means, scripts that relied on default values (previously, v_call="V_CALL"), will now fail if calls to the functions are not updated to reflect the correct value for the data. If data are in the Change-O format, the current default value v_call="v_call" will fail to identify the column with the V gene calls as the column v_call doesn’t exist. In this case, v_call="V_CALL" needs to be specified in the function call.ExampleDb converted to the AIRR Rearrangement standard and examples updated accordingly. The legacy Change-O version is available as ExampleDbChangeo.GRAVY to gravy);countGenes, countClones (e.g., SEQ_COUNT to seq_count)estimateAbundance (e.g., RANK to rank)groupGenes (e.g., VJ_GROUP to vj_group)collapseDuplicates and makeChangeoClone (e.g., SEQUENCE_ID to sequence_id, COLLAPSE_COUNT to collapse_count)summarizeTrees, getPathLengths, getMRCA, tableEdges, testEdges) also return columns in lower case (e.g., parent, child, outdegree, steps, annotation, pvalue)IG_COLOR names converted to official C region identifiers (IGHA, IGHD, IGHE, IGHG, IGHM, IGHK, IGHL).General:
baseTheme looks is now consistent across sizing options.cpuCount will now return 1 if the core count cannot be determined.padSeqEnds wherein the pad_char argument was being ignored.Diversity:
estimateAbundance slot clone_by now contains the name of the column with the clonal group identifier, as specified in the function call. For example, if the function was called with clone="clone_id", then the clone_by slot will be clone_id.Lineage:
buildPhylipLineage arguments vcall, jcall and dnapars_exec to v_call, j_call and phylip_exec, respectively.Deprecated:
rarefyDiversity is deprecated in favor of alphaDiversity, which includes the same functionality.testDiversity is deprecated. The test calculation have been added to the normal output of alphaDiversity.General:
ape and tibble dependencies.Lineage:
readIgphyml to read in IgPhyML output and combineIgphyml to combine parameter estimates across samples.graphToPhylo and phyloToGraph to allow conversion between graph and phylo formats.Diversity:
estimateAbundance where setting the clone column to a non-default value produced an error.estimateAbundance through the min_n, max_n, and uniform arguments.estimateAbundance. alphaDiversity will call estimateAbundance for bootstrapping if not provided an existing AbundanceCurve object.DiversityCurve and AbundanceCurve objects to accomodate the new diversity methods.Gene Usage:
groupGenes now supports grouping by V gene, J gene, and junction length (junc_len) as well, in addition to grouping by V gene and J gene without junction length. Also added support for single-cell input data with the addition of new arguments cell_id, locus, and only_igh.General:
nonsquareDist function to calculate the non-square distance matrix of sequences.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:
fill argument to countGenes. When set TRUE this adds zeroes to the group pairs that do not exist in the data.groupGenes to group sequences sharing same V and J gene.Toplogy Analysis:
indirect=TRUE.makeChangeoClone will now issue an error and terminate, instead of continuing with a warning, when all sequences are not the same length.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.